I agree with using a rust-free body whenever possible. Save the rust repair money for a really nice paint-job and hipo parts!
I wouldn't exactly give up on the T-Tops though...I believe that they were engineered as a kit, so if you can get the kit out of one car in good condition, you have a good chance of putting them back into another car.
It will be a butt-load of work though...plan on taking lots of notes, pics, and measurements. Getting the kit parts reinstalled in the right order and in the right positions will mean the difference between leaks and no leaks.
You might want to look around for a local shop that has done T-Top kits in the past. Somebody that does aftermarket sunroofs, etc.
We could use a good picture reference for the parts and assembly of the MII T-Tops. Hint, hint.
78CobraII