The truck that the TH400 came out of could answer your question. Long wheel base trucks (long bed) had an extra three inches added to the end of the TH400 tranny. Short wheel base trucks (short bed) didn't and can be used in a car. You can use the longer tranny but you have to shorten the drive shaft. Heavier duty trucks (one ton and up had a bolt on yoke instead of a slip yoke, but it can be modifided with a little work to accept a slip yoke by disassembly of the tail shaft and grinding down the O-ring collar).
There are internal differences as well reflecting the GVW of the vehicle. A tranny rebuilder can combine the best of the 1965-'69 with the 1975 and up TH400 internal parts (sprags and pistons, etc.) to make a bullet proof monster that will work in a car.
No difference in drive shaft between convertible and other two door cars. Drive shafts interchange. BUT, the end of the drive shaft is different between a TH350-PowerGlide car and one with a TH400. The TH400 was a bigger (physically) and stronger (made of cast iron instead of aluminum) transmission; as such it had a bigger stronger rear yoke to fit the bigger stronger out put shaft. You have to match the yoke to the output shaft size (spline count).