If the car was a four, then it should have a deep fan shroud on the radiator. You will not use this with the six cylinder engine since the engine sits close enough to the radiator not require the shroud's use. Keep the radiator, it's the same regardless of the engine.
If the Jeepster setup is anything like what was used in the Henry J, the front motor mount brackets from the engine to the frame differ as well (my parts books are packed for a move so I cannot verify) and if they are you'll need to source a pair of them.
The transmission looks correct. It should be a T96.
Attached is a picture of my Jeepster. It was the last known assembled unit.