Re: manual transmission wanted
You'll need to get a suitable flywheel, as jas mentioned.
Also a pilot bearing (I believe that's the spigot bearing he talked about), which goes in the back of the crank.
The 5.0 is externally balanced, so when you select a flywheel, be sure it has the 50oz imbalance (as opposed to 28oz).
If you're planning to just drive it around, the V6 T5 will hold fine, but if you're planning on running it, it'll be nice to see how long it holds up. Then, again, most hot rods are much lighter than stock Mustangs, so maybe it'll balance out.
I'm almost positive you're going to need a new bellhousing and input shaft, but I can't remember right off. Is the engine in the car already? If it's not, simply snug the transmission to the back of the engine. If it fits tight all around and the bolt holes line up, you won't need a new bellhousing. If the bolts don't line up, you'll need a new one. If you need a new bell, you'll very likely to need a new input shaft, but don't hold me to that.