If you want to have similar end gearing as the supra, you can get a 3.07 ratio diff or a 2.93 diff. That last one 'll do about 2600rpm at 80mph.
I think the difference between 3.23 and 3.46 would be quite small.
I dont know how much power and torque you're going to put down, but there's no use in having a 1st gear so short that its totally unusable. If you're going to make big torque figures, you even risk breaking traction all the time in 2nd.
Usually the more torque down low you make (say in the range of 2k-4krpm), the lower the final drive (with the same gearbox)
Too bad there is no realistic way to change the gearbox ratio's, to get for instance a ration patternt like a s2000 has (relative long 1st and ratio's get shorter when gears get higher). That would be ideal but very costly.
Be sure to choose your final drive ratio before for example buying a LSD because the different ratio's require different lsd's.
I'm not sure but 3.23 and 3.46 might use the same setup, but 3.07/2.93 use a different setup.
A 3.62 z4m diff is incompatible (210 diff instead of 188 diff) and requires a different rear axle (subframe, driveshafts, trailing arms the lot...) and propshaft.
I also think it depends on your use; if you're planning to do a roadtrip/vacation in this car you'll get crazy if you have to listen to 3500rpm for hours on end on the highway
