the first issue you are going to have it the engine mounts. you may be able to use the stock early chassis mounts from a 65 model year, and use the late model engine mounts from a mustang, since both use a single bolt to mount to the chassis.
the next thing is that you are going to have to use a 164 bell housing since the 3.8 uses the AOD trans. this assumes you want to use an early transmission.
one thing to be aware of, the 3.8 V6 block came in two versions, front wheel drive, and rear wheel drive. the mounting systems are different on each block and they will NOT interchange. they do however still use the same cylinder heads, flexplate/flywheel, intakes, etc. so make sure your block comes from a rear wheel drive car if you are just shopping for the basic engine without a donor car.