I agree that when it comes to domestic Ford products, the differential, uprights, drive axles, etc. are not the areas typically associated with quality problems. And if I'm remembering correctly, the t-bird can interchange quite a bit of the front end hardware with certain variants of the mustang, and even some pure racing applications.
The t-bird IRS can be found with an aluminum housing (8.8"?) and a limited slip can be added if your chosen donor doesn't come with one. Also using the Ford 8.8 opens up a wide range of gear ratios that can be installed into that differential.
All of that said, the main reason I recommended the t-bid set-up over a Miata based donor is the brakes. With a t-bird you can upgrade into Mustang based brakes - big brakes for a big, heavy car. With a Miata, you're pretty much stuck with OE Miata brakes in back and one or two expensive big brake kit choices for the front. I don't know if you've spent much time in the pits talking with spec Miata guys, but quite a few of them complain about the brakes.
While you would be working with less mass than a stock Miata, velocity can become a much bigger factor in brake performance than mass at a very rapid rate. Probably not too much of an issue at autocross speeds for single laps, but on a big track with repeated lapping and hard braking, it's not hard to overcome the mass available in a braking system with heat and cook the whole mess 'till it stops working. The Ford system will offer much more initial mass and surface area to both soak and dissipate that heat. And there are lots of racing specific brake parts available for the Ford parts at very reasonable (for racing) prices.
At stock power with your chosen S2000 engine you may already be past what the Miata brakes can manage over the length of a full lapping session. I've been in a turbo Miata with well developed street brakes (but running racing pads), and that car (with about 240 whp) was running into significant brake fade on lap 3 at our local track. Big power requires big brakes .. squared.
For the record, I've always found running out of power to be far less dramatic than running out of brakes...
Thank you for all of your input you are obviously very knowledgeable about this type of thing. I think I am going to go with the Supra at the moment. With the price being $800 and the body is in good shape I think I can just about break even and get a free suspension/brake/steering/wheel setup. If it turns out to not be worth the hassle I can sell the wheels/rear end and turn a profit.
I looked at the front suspension at it is double wish bone, also it is the turbo version of the Supra so the brakes are built for a car with 230 HP. I will not be able to get 13" wheel like I wanted but I have a set of 17" wheels that weigh ~16lb and already have race tires so that will save some cash. That will also help with longer gearing for autocross.
My main goal for the car is autocross, the MKII model would be if I wanted to become Nationally competitive. I would have to get there and see what my car lacks and what everyone else is doing to make their cars fast then build a car to beat them. I think that is not a realistic goal at the moment. I will trailer the car to the track initially but once it is running I will start to tune and optimize it to make it fast, then make it road legal. Weight is not going to be an issue as the F22C puts me in E-Mod with and 1800lb minimum weight. I might even add a stereo at that point.