Nice work so far.
I also have been planning a 3.8 S/C build using Miata based suspension. I'm getting close to starting, but I also have a Subaru affliction that keeps suckering me over.
I chose to use a second generation RX7 differential. It's the same as a '94+ Miata diff, but has a longer nose on it so you don't have to mess with a Powerplant frame. The RX7 diff will accept Miata axles, has a clutch-type LSD (vs. Torsen) and (for me) was way cheaper. There is also a turbo version that should have no problems with the T-bird motor.
To deal with the Mazda diff ratio, I upgraded the cam. I told CompCams I really wasn't interested in more power, but wanted to raise the powerband to a higher RPM. I trust what they sent me, but we'll see
. I upgraded the valvesprings and retainers for the RPM increase. I had the rotating assembly balanced, and had the valves unshouded a bit for slightly better flow. I also picked up some secondhand lightened pullies, lightened flywheel and the larger '94-'95 S/C pully to slow down the blower. Along with 'larger than Miata' wheels, I think I'll be OK with the revs. But with a factory rating of 210HP and 315 Ft/lbs (before any upgrades) I do expect first gear to be completely optional.
I've collected quite a bit of literature (and SuperCoupe knowledge) for my project, so feel free to ask any questions you may run into.
I've got good wiring diagrams for the '90 model year. Lots of good reading over here:
http://www.sccoa.com/forums/