The axles are different. The radiator on the NA is smaller. I accomplished the full swap, but it took getting a wrecked turbo and swapping all the wiring from the headlights to the taillights. This is a HUGE undertaking. Also because I used '91 turbo wiring the JDM ECU would not work. Do not expect the swap to be easy or cheap. Good luck.
I thought of another problem...the assembly that holds the throtle cable (it mounts next to the intercooler) is slightly different. I didn't notice this until it had almost rubbed all the way through my intercooler (bad). Also the 3sgte weighs about 300lbs more than the 5sfe and it made me notice how badly I needed new shocks. I do admit, the car is amazing with the 3sgte over the NA.
the USDM shift linkage from the NA MR2 will not work with the JDM trans. u must use the Turbo JDM linkage. US linkage will not allow u to go into 5th and reverse, i just had this problem yesterday i have done the swap, have any of u guys done this swap to be able to actually tell people what works and what doesnt?