well you are going to need a double hump tranny mount for 1 thing. You are going to need a set of headers and a h-pipe and the cat back exhaust from a 5.0L. you need the engine mounts from a 5.0L. You are going to have a hard time installing the c-6. Better to find a auto (AOD4) out of a wrecked 5.0L and the driveshaft. Also find yourself a 8.8 rear end as your car only has a 7.5.
Please sort out the question. Your 85 Mustang 2.3 is easy to swap to either an efi or carbed 5.0. You need the 5.0 engine and trans. While the 4 speed might be able to be bolted up to a 5.0, with the correct belhousing, and may fit a T5 bell, it will take more work that it may be worth.
Your best trans are a T5, a C4 or and AOD. The C6 can be done, but it is supposedly a very tight fit in the trans tunnel, and it weighs about 100 lbs more than a C4. It is a mother to horse up in place. Been there, done that.
You can send all the leftover 4 cyl parts to me, I have an 85 2.3 auto that could use a running 2.3.