Auto to Manual Swap, Wiring, Ecu, CC, NSS, CLSW, Trac, Snow, now smogged in CA! - Lexus IS Forum
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post #1 of 138 (permalink) Old 09-01-2011, 10:58 AM Thread Starter
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Auto to Manual Swap, Wiring, Ecu, CC, NSS, CLSW, Trac, Snow, now smogged in CA!

When looking for information about doing a transmission swap, there was some questions that i could not get answers to. My goal was to have a full working swap that was CEL free, and had the look and feel of a factory car. Here is how I did it.

Here is my basic parts list using all stock parts

w55 transmission
shifter
Slave cylinder
Clutch Pedal
Clutch Line
Shift boot
Flywheel
Manual brake pedal
Manual drive shaft
Rear engine “transmission” mount
Stock Shift knob
Manual Steering Wheel
Manual Cluster
New pressure plate & clutch disk
M/T Ecu


Uninstalling the automatic transmission, I followed this basic information from All Data.


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Removing the Automatic Transmission

1. REMOVAL
2. REMOVE LEVEL GAUGE
3. REMOVE FILLER PIPE Remove the bolt and filler pipe with the O-ring.

3. REMOVE AIR CLEANER, MAP METER AND INTAKE AIR CONNECTOR PIPE ASSEMBLY
4. REMOVE EXHAUST MANIFOLD WITH TWC
a. Disconnect the 3 connectors.
b. Remove the 8 nuts, 2 gaskets and exhaust manifold with the TWC. Torque: 39 Nm (400 kgf-cm, 29 ft. lbs.)
5. RAISE VEHICLE
NOTICE: Make sure that the vehicle is securely supported.
6. REMOVE NO. 1 AND NO. 2 ENGINE UNDER COVERS
7. REMOVE LH FRONT FLOOR CENTER COVER
8. REMOVE NO. 1 REAR FLOOR BOARD
9. DRAIN ENGINE COOLANT
10. REMOVE UPPER RADIATOR HOSE FROM RADIATOR
11. REMOVE FRONT AND CENTER EXHAUST PIPES
12. REMOVE SHIFT CONTROL ROD
a. Remove the nut and washer, and disconnect the rod. Torque: 13 Nm (130 kgf-cm, 9 ft. lbs.)
b. Remove the nut and shift control rod. Torque: 13 Nm (130 kgf-cm, 9 ft. lbs.)
13. REMOVE PROPELLER SHAFT
14. DISCONNECT OIL COOLER PIPE
a. Remove the 3 bolts and 3 clamps. Torque: 5.4 Nm (55 kgf-cm, 48 inch lbs.)
b. Loosen the 2 union nuts from the transmission. Torque: 44 Nm (450 kgf-cm, 33 ft. lbs.)
NOTICE: Be careful not to damage the oil cooler pipe.
c. Disconnect the 2 oil cooler pipes from the transmission.
15. REMOVE TORQUE CONVERTER CLUTCH MOUNTING BOLT
a. Remove the hole plug.
b. Turn the crankshaft to gain access to each bolt.
c. Hold the crankshaft pulley nut with a wrench and remove the 6 bolts. Torque: 48 Nm (490 kgf-cm, 35 ft. lbs.)
16. SUPPORT TRANSMISSION WITH JACK
17. REMOVE 4 ENGINE REAR SUPPORT MEMBER SET BOLTS Torque: 25 Nm (260 kgf-cm, 19 ft. lbs.)
18. DISCONNECT CONNECTORS AND WIRE HARNESS
a. Tilt down the transmission.
NOTICE: Take care so that the cooling fan does not come in contact with the fan shroud.
b. Disconnect the following connectors:
1. O/D direct clutch speed sensor connector
2. Vehicle speed sensor connector
3. Park/neutral position switch connector
4. Solenoid connector
c. Disconnect the wire harness from the clamps on the transmission.
19. REMOVE STARTER
a. Disconnect the connector and wire from the starter.
b. Remove the 2 bolts and starter. Torque: 37 Nm (380 kgf-cm, 27 ft. lbs.)
20. REMOVE TRANSMISSION Remove the 9 bolts, ground cable and transmission.
Torque:
17 mm head: 72 Nm (730 kgf-cm, 53 ft. lbs.)
14 mm head: 37 Nm (380 kgf-cm, 27 ft. lbs.)


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TUNNEL MODIFICATION

Tunnel Modification

The Automatic transmission tunnel is about 1 inch lower than the manual tunnel, so to make clearance for the manual transmission this is how I changed the tunnel.

Got a used manual tunnel for free, traced where I wanted to make my cuts

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marked where I wanted to cut the auto tunnel

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test fit and painted “missed painted picture”

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Forgot a picture, but drilled and placed rivits, then put down some seam sealer.

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and finally installed the rivets.

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CLUTCH MASTER CYLINDER INSTALLATION

I trace a outline of the area cut out on the firewall on a piece of card stock, I just use junk mail, then center the clutch master cylinder on it to make a template.

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then trace it to the firewall

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then cut, and paint the raw metal

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and install the CMC

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CLUTCH PEDAL ASSEMBLY

A manual clutch and brake pedal assembly is required for a swap, at the time I could not find a used set for a reasonable price so I bought the parts new from amayama trading. Here is how to assemble.


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I know there is a clutch pedal thread here on the forum, but it is mostly incomplete, so here is a little more info

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I do not have the proper names for everything so just hang in there.

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Install plastic bushing

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followed by metal busing

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install the pedal stop

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install spring clip

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install clucth master cylinder retianer

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install busing

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spring, “I use grease on mine to prevent squeaky noises”

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this thing, with c clip

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and larger spring, with more grease

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so then I thought I would modifiy my orginal brake pedal. Traced out the shape of the manual pedal, installed it and realized that it still wasnt right, way to far left. Cut my losess and ordered another pedal.

And finally 3 pedals again

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1. INSTALL TRANSMISSION
a. Raise the engine front side.

b. Install pilot bearing.
c. install flywheel.
d. install clutch disc and pressure plate.
e. Align the input spline with a clutch disc and install the transmission to the engine.
HINT: Turn the transmission a little in the clockwise and jack up until just before the transmission housing touches the body.
c. Install the transmission and wire harness clamp with the 8 bolts. Torque:
Bolt A (12 mm head bolt): 71.6 Nm (730 kgf-cm, 53 ft. lbs.)
Bolt B 110 mm head bolt): 37.3 Nm (380 kgf-cm, 28 ft. lbs.)
2. INSTALL ENGINE REAR MOUNTING Install the engine rear mounting with 4 the bolts.
Torque: 25.5 Nm (260 kgf-cm, 19 ft. lbs.)
3. INSTALL REAR ENGINE MOUNTING MEMBER Install the rear engine mounting member with the 4 bolts and 4 nuts.
Torque:
Bolt: 25 Nm (255 kgf-cm, 18 ft. lbs.)
Nut: 13.5 Nm (138 kgf-cm, 10 ft. lbs.)
4. INSTALL STARTER
a. Install the starter with the 2 bolts. Torque: 37.3 Nm (380 kgf-cm, 28 ft. lbs.)
b. Install the wire with the nut. Torque: 9.8 Nm (10 kgf-cm, 7 ft. lbs.)
c. Connect the connector.
6. CONNECT BACK-UP LIGHT SWITCH CONNECTOR
7. CONNECT CLUTCH RELEASE CYLINDER, CLUTCH LINE BRACKET AND EARTH WIRE
a. Connect the clutch line and earth wire with the bolt. Torque:
Bolt A: 37.3 Nm (380 kgf-cm, 28 ft. lbs.)
b. Connect the clutch release cylinder with the 2 bolts. Torque:
Bolt B: 11.7 Nm (119 kgf-cm, 9 ft. lbs.)
8. INSTALL PROPELLER SHAFT
9. INSTALL FRONT AND CENTER EXHAUST PIPES
10. FILL WITH TRANSMISSION OIL Torque:
Filler and Drain plug: 38 Nm (387 kgf-cm, 28 ft. lbs.)
Oil grade: API GL-4 or GL-5
Viscosity: SAE 75W-90
Capacity: 2.6 L (2.7 US qts, 2.3 Imp. qts)
11. INSTALL NO. 1 REAR FLOOR BOARD
12. INSTALL LH FRONT FLOOR CENTER COVER
13. LOWER VEHICLE
14. INSTALL EXHAUST MANIFOLD
a. Install 2 new gaskets to the cylinder head.
b. Install the exhaust manifold with the 8 nuts. Uniformly tighten the nuts in several passes. Torque: 40 Nm (408 kgf-cm, 29 ft. lbs.)
c. Connect the heated oxygen sensor (bank 2 sensor 1) connector.
d. Install the case clamp.
15. INSTALL INTAKE AIR CONNECTOR
a. Install the intake air resonator to the throttle body, tighten the 2 hose clamp bolts.
b. Connect the PCV hose to the No. 2 cylinder head cover.
c. Connect the engine wire harness clamp to the air cleaner case.
d. Connect the MAP meter connector.
16. CONNECT RADIATOR UPPER HOSE NO. 1 FROM ENGINE
17. FILL WITH ENGINE COOLANT
18. INSTALL ENGINE COVER NO. 1 Torque: 5.0 Nm (51 kgf-cm, 44 inch lbs.)
19. INSTALL NO. 1 AND NO. 2 ENGINE UNDER COVERS
20. INSTALL TRANSMISSION SHIFT LEVER
a. Install the washer.
b. Apply MP grease to the tip of shift lever.
c. Install the shift lever with the 4 bolts. Torque: 8.0 Nm (82 kgf-cm, 71 inch lbs.)
21. INSTALL SHIFT BOOT
22. INSTALL SHIFT BOOT RETAINER
a. Install the shift boot retainer with the 4 bolts.
b. Connect the 2 wire harness clamps.
23. INSTALL UPPER CONSOLE PANEL AND CONSOLE BOX
24. DO ROAD TEST Check for abnormal noises and smooth shifting.


WIRING

ECU
The removal of the automatic transmission gives you around 10 CEL all transmission related. I picked up M/T ECU which does plug straight in “02+”, but I required reseeding since I did not get a master key. The dealership reseeded the ecu to my keys. 1 hour $130. This ultimately did not rid the CEL, 1 code for speed signal remained. Speed signal works as the following shows.

Auto
A/T ----------> ECU.
Trac ----------> Combo meter

Manual
M/T ----------> Combo meter
Combo Meter ----------> ECU

A converted car will work like this

Trac------------> Combo Meter
Combo Meter -------> ECU

So now we know we need to get the speed signal from the combo meter to the ECU here is how to do it.

ECU speed signal. Insert pin in combo meter harness A13 wire to ECU connector B11.


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So now we have speed our CEL taken care of, lets do the neutral safety switch, and reverse light. This is the old connector from the automatic transmission that we need to use some wiring from. The actual numbers are on the connector.

REVERSE LIGHT


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Reverse light. So from the old A/T wiring, take #2 and #3 And wire into new harness Part number 90980-11142. Then simply plug into reverse light plug on the transmission.*

NEUTRAL SAFETY SWITCH

Neutral safety switch. Reroute wire #6 and #9 to the the clutch pedal. connect wire 6 & 9 to Neutral safety switch. Part number 90980-10825


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CRUISE CONTROL

Cruise control clutch switch. Cut B13 from ecu and wire to cruise control clutch switch, then to driver side fuse box harness 1A pin 4. Part number 90980-10906.


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Used wire protective wrap for wires from ecu and NSS. There is a nipple on the main grommet on firewall, i cut the tip off to feed my wires through.


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Didn't want to make holes in ecu box, turns out there is one already by front right corner.


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TRACTION AND SNOW.

the pwr/snow button as you know is part of the auto shift assembly, on stock manual it is a two part trac off/snow under the radio and next to heated seats if your is so equipped. luckily most of the wiring is already where you need it. there is one wire you need to extend and that is the black and yellow wire that goes to your old pwr/snow button.

your stock wiring, as you compare to the next photo, you can clearly see only one wire needed black yellow.


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this photo is courtesy of solidsnake. you can see that the wiring is not in the same order as the traction only button, so make sure your order is right. Also you may note that you need a 6 pin plug versus the 4 pin plug, i dont have the part number yet but will update when i do.


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there was some speculation that the old pwr/snow button will work in for the trac/snow button. It does to a point, there will need to be some trimming of your "bezel" to make it work, and also i noticed you need to pushing the button is differnt, it doesnt click out the same. it would be best to just source a traction/snow button. but here is mine temporarily.

***Update, i never put these two pieces of the puzzle together, you know how the the pwr button has a memory for the automatics, so once you turn your trac to a pwr button every time you start your car it will automatically have traction turned off! i will now keep it in instead of replacing it!******


Update 11/08/12 this is probably going to be my last update mainly because there was only one real missing piece to the puzzle. Some questioned the legality of changing the transmission and being able to pass smog here in California with there strict laws. Well my registration renewal was finally due with a updated smog check. took it in and passed without a problem. It even notes that it is a manual transmission on the print out.


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02 CW Sportcross rebuild in progress
02 BO Sportcross 2jzgte build in progress
11 SW Tundra DC TRD supercharged
02 MSM L-tuned Sportcross 5 Speed Sold

Sportcross owners group on facebook

My Story: http://my.is/forums/f219/sportcross-...8/#post7991882


My For Sale: http://my.is/forums/f99/sportcross-s...hifter-438917/

Last edited by Curran; 12-31-2015 at 01:09 PM. Reason: update
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post #2 of 138 (permalink) Old 09-01-2011, 05:40 PM
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Great write up!
I'm planning to do the same thing to my IS.
Can you elaborate more on the tunnel part? were you able to use the stock boot? what exactly did you do and use?

Thanks!!!

2004 Savannah Metallic IS300 E-Shift 5AT->Now 5MT. M85 Torsen LS Differential, Supra BBK.
2005 Graphite Gray Pearl IS300 all stock (fiance's)
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post #3 of 138 (permalink) Old 09-01-2011, 08:29 PM
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Nice work! +rep

-Jimmy
2001 IS300 Black Onyx with '04 motor swap and MT.
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post #4 of 138 (permalink) Old 09-03-2011, 08:27 PM Thread Starter
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Quote:
Originally Posted by Solid_Snake View Post
Great write up!
I'm planning to do the same thing to my IS.
Can you elaborate more on the tunnel part? were you able to use the stock boot? what exactly did you do and use?

Thanks!!!
So you asked enough times so i updated the step with more pictures.

02 CW Sportcross rebuild in progress
02 BO Sportcross 2jzgte build in progress
11 SW Tundra DC TRD supercharged
02 MSM L-tuned Sportcross 5 Speed Sold

Sportcross owners group on facebook

My Story: http://my.is/forums/f219/sportcross-...8/#post7991882


My For Sale: http://my.is/forums/f99/sportcross-s...hifter-438917/
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post #5 of 138 (permalink) Old 09-03-2011, 08:40 PM
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i wrote one of the 2 threads you linked in your post, so i didn't read through your entire write-up, since i've already done it, but WOW!! seems amaazing!!

do you have any pictures of how it looks finished? congrats on doing it so well!

©2006 my.IS
IS300 '01 - Spectra Blue Mica | ELIXIR | SRT 2.75 Turbo | V161 6-speed | Volk GT-M | Tein CS |

IS F '12 - Ultrasonic Blue Mica | ISS Forged Exhaust | WALD Diffuser | Ventross Trunk | Lexon Roof Spoiler |
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post #6 of 138 (permalink) Old 09-03-2011, 09:00 PM
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Thank you so much for posting the information about the shifter. I really appreciate it.

2004 Savannah Metallic IS300 E-Shift 5AT->Now 5MT. M85 Torsen LS Differential, Supra BBK.
2005 Graphite Gray Pearl IS300 all stock (fiance's)
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post #7 of 138 (permalink) Old 09-03-2011, 09:02 PM Thread Starter
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Quote:
Originally Posted by LO 21 View Post
i wrote one of the 2 threads you linked in your post, so i didn't read through your entire write-up, since i've already done it, but WOW!! seems amaazing!!

do you have any pictures of how it looks finished? congrats on doing it so well!
yes, i read your thread numerous times. I wish i had a lift when doing mine, lucky. and your car looks amazing. I will have to get some pics up, right now im finishing up painted tails.

02 CW Sportcross rebuild in progress
02 BO Sportcross 2jzgte build in progress
11 SW Tundra DC TRD supercharged
02 MSM L-tuned Sportcross 5 Speed Sold

Sportcross owners group on facebook

My Story: http://my.is/forums/f219/sportcross-...8/#post7991882


My For Sale: http://my.is/forums/f99/sportcross-s...hifter-438917/
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post #8 of 138 (permalink) Old 09-03-2011, 10:46 PM
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Quote:
Originally Posted by Curran View Post
yes, i read your thread numerous times. I wish i had a lift when doing mine, lucky. and your car looks amazing. I will have to get some pics up, right now im finishing up painted tails.
damn, can't imagine how tricky that must have been with no lift!

thanks for the kind comments. car is going through some aesthetic changes now, but the process is slow cuz i haven't really had time to get things done in the past few months.

i can't imagine my thread being extremely helpful, besides for gathering parts, since my swap was an 01, and yours being an 02 obviously required a lot more wiring. but what you did is quite impressive! very detailed.

after the manual to r154, i actually swapped the r154 for a v161 supra 6-speed over a year ago though. amazing transmission.

if i may recommend, you should look into a Karl Sport Short shifter.
i almost swapped a stock tranny JUST so i could have this shifter.
his re-design includes a thicker and stronger shaft, the shifter, from what i can imagine, is out of this world. not sure if they're even available any more, they were designed and produced by a member here on the forum, and he only made a small amount. but look into it nonetheless.

©2006 my.IS
IS300 '01 - Spectra Blue Mica | ELIXIR | SRT 2.75 Turbo | V161 6-speed | Volk GT-M | Tein CS |

IS F '12 - Ultrasonic Blue Mica | ISS Forged Exhaust | WALD Diffuser | Ventross Trunk | Lexon Roof Spoiler |
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post #9 of 138 (permalink) Old 09-07-2011, 11:48 AM Thread Starter
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Quote:
Originally Posted by LO 21 View Post
if i may recommend, you should look into a Karl Sport Short shifter.
i almost swapped a stock tranny JUST so i could have this shifter.
his re-design includes a thicker and stronger shaft, the shifter, from what i can imagine, is out of this world. not sure if they're even available any more, they were designed and produced by a member here on the forum, and he only made a small amount. but look into it nonetheless.

It seems like those shifters are prone to failure? was looking at a thread showing how they snap in half. I dont really like the height of the stock shifter, if it could lose a couple inches it would look much better, but i dont want the extra noise associated with aftermarket ones, and snapping in half? forget about it. I think i will stick with the stock one for now. I might consider going to a v160 someday, are you still on auto diff? what is you rpm at 65mph. With the w55 and auto diff, im at 3k.

02 CW Sportcross rebuild in progress
02 BO Sportcross 2jzgte build in progress
11 SW Tundra DC TRD supercharged
02 MSM L-tuned Sportcross 5 Speed Sold

Sportcross owners group on facebook

My Story: http://my.is/forums/f219/sportcross-...8/#post7991882


My For Sale: http://my.is/forums/f99/sportcross-s...hifter-438917/
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post #10 of 138 (permalink) Old 10-21-2011, 10:21 AM
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I love you.

Manual swap on my mom's SportCross starts next weekend

Migs

__________________________
2002 AR IS300 5-speed w/LSD
/TTE Coilovers/Eibach Sways/Endless pads/Work Equip 05's/Wald blah blah blah

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post #11 of 138 (permalink) Old 10-21-2011, 03:59 PM
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Best IS300 AT to MT write up evar!

2001 SY E-Shift
-HKS Hi Power
-Megan EZ Street Coilovers
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-Fig's LCA and Toe Rods
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post #12 of 138 (permalink) Old 10-22-2011, 09:36 AM Thread Starter
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Quote:
Originally Posted by Migs View Post
I love you.

Manual swap on my mom's SportCross starts next weekend

Migs
It's about time, to think when i started this I was PMing you for info. Good luck.

Quote:
Originally Posted by Sexy_Ninja View Post
Best IS300 AT to MT write up evar!
Thank you.

02 CW Sportcross rebuild in progress
02 BO Sportcross 2jzgte build in progress
11 SW Tundra DC TRD supercharged
02 MSM L-tuned Sportcross 5 Speed Sold

Sportcross owners group on facebook

My Story: http://my.is/forums/f219/sportcross-...8/#post7991882


My For Sale: http://my.is/forums/f99/sportcross-s...hifter-438917/
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post #13 of 138 (permalink) Old 10-24-2011, 03:47 PM
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Brandon I have the wiring for the TRAC/SNOW switch and connector part number if you still need it.

2004 Savannah Metallic IS300 E-Shift 5AT->Now 5MT. M85 Torsen LS Differential, Supra BBK.
2005 Graphite Gray Pearl IS300 all stock (fiance's)
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post #14 of 138 (permalink) Old 10-24-2011, 06:10 PM Thread Starter
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Quote:
Originally Posted by Solid_Snake View Post
Brandon I have the wiring for the TRAC/SNOW switch and connector part number if you still need it.
Sounds good Alvaro lets just get this thing 100% complete so everyone can benefit.

02 CW Sportcross rebuild in progress
02 BO Sportcross 2jzgte build in progress
11 SW Tundra DC TRD supercharged
02 MSM L-tuned Sportcross 5 Speed Sold

Sportcross owners group on facebook

My Story: http://my.is/forums/f219/sportcross-...8/#post7991882


My For Sale: http://my.is/forums/f99/sportcross-s...hifter-438917/
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post #15 of 138 (permalink) Old 01-23-2012, 07:34 PM
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How about the Auto transmission oil cooler pipes that connect to the radiator? Do those just get removed or does the manual have a place for them? I didn't see anything in the shop manual about it.
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