if you are trying to bolt it to the stock bellhousing of a V8 powered 65 mustang(all mustangs built in 1964 are titled as 1965 cars), you are going to have a problem if the bellhousing is original as it is a 5 bolt pattern bell, and the 94 uses a 6 bolt bell. if you are also swapping the transmission, then you need to change the transmission crossmember. if you are using a six bolt bell, and a C4 trans, then you have no issues. if you are using the 6 bolt bell and a manual trans, then you need a part to allow the use of the "Z" bar on the early car as there is no hole for the "Z" bar pivot point on the block. there is a bolt on pivot point though available from a number of mustang parts suppliers.
If the 64 was a 289, it'll be a snap - otherwise, you'll have to get motor mounts and such - but it shouldn't be too big a hassle.
Check to see if it had an early engine (5 bolt bell housing vs. later 6 bolt) This isn't an issue if you're using the later transmission and engine.