I thought it was the noise that you were describing. If you have new brake rotors/pads and the shaking is still there, then it's the No.2 control arms that are causing the shaking. Mine does the same thing, even with new tires. I've yet to order my Figs replacement bushings.
When you're braking, you put a lot of stress on the No.2 bushing. If yours is as bad as you say, then this is definitely the cause of the shaking.
02' Manual w/MKIII LSD and no sunroof.