With all the modifications you mentioned it will be a very fun car that that handles but feels more like a refined muscle car compared to the M3. I can't comment from experience on the 1UZ+W58 specifically but with very similar modifications to my SC300 5-speed with 4.272 gears, a Torsen LSD and suspension it's a lot of fun. I'd like another 50-100 horsepower from it and I'd be truly happy.

Any 92-97 SC400 is going to have 25-35 more horsepower and a totally different torque curve. Any 98-00 SC400 is going to have a very respectable near 300hp (crank) and more torque than the earlier 1UZ-FE's.

It is possible to swap a W58 or R154 onto a 98-00 SC400 and defeat the CEL light issues. If this interests you, look up threads written by Cartmill detailing the CEL electrical fixes he applied to his 1998 SC300 with a W58 manual swap. Very tedious but it has been done.

Ultimate handling performance is not going to be in M3 territory but that said you can make the SC handle VERY well without turning it into a drifter. One key element is buying a good set of tires like BFGoodrich T/A KDW2's, BFG Comp2's or Bridgestone S-03's. Also a good suspension that isn't specifically a drift coil over. I recommend the Gixxer_Drew suspension listed on supraforums in spring rates of 500/250 or the more aggressive 600/325 if you're okay with a slightly rough ride on poorly maintained road surfaces.

If you really want something fun and can hold out for one, find 98-00 SC400 VVT-i and do all the modifications you listed. Just read Cartmill's threads FIRST.