well for starters, the biggest is one engine is designed to be longitudinally mounted engine with a transmission behind it, the other is a transversely mounted engine with a transaxle mounted beside it. at least in other cars, while the engine is extremely similar, the external block has some minor differences, for instance, you cant use a continental 4.6 in a mark VIII or mustang.
as such, there could be many things that may just be different enough to make it not fit right in... like motor mounts, or bell housing bolts, or even where the front drive accessories may be mounted.