Since you will be adding a supercharger in the future, I would go with the 3.55's. Good street manners, good highway gas mileage and enough gear to get you down the track in reasonable fashion.
As for the TB, I think the Holley intake has a 70mm opening , but I am not sure on this. If it does, then you might as well go with the 70mm. I wouldn't go any bigger unless you are going to make your Stang into a drag-only type machine.
Congratulations on your purchase!

E
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1991 5.0 LX Coupe - 38,000 miles
13.17 @ 106.14 mph w/ 2.138 60'
[This message has been edited by 302 LX Eric (edited 06-25-2001).]