So I recently bought 2 shit missiles
 

I recently bought 2 07 Honda fits. One has a rotted rear end one needs engine mounts, could I use them like legos and put the body of the shot one on the clean frame? Or do I need too gut then swap over the internals?

Unibody vehicles aren't really the same as a body-on-frame vehicle like a truck where the removal of a handful of large bolts (basically) allows you to remove the cab or bed.

Installing new engine mounts is way easier than trying to repair bad rust damage. That's what I would do.