Of course it will, its the same engine compartment as the 64 that they built the Thunderbolts out of. It does take some clearancing of the shock towers and a few other things, but it by no means needs a full chassis to work.
And what's even crazier is that after the shock tower modifications, there's more room for spark plug and header access than any unmodified Mustang.
A good friend of mine just bought a '63 Fairlane 500 with a 221 and 3 speed about a month ago. I'm already working on him to do this very swap, and it won't take much to convince him since he's a Ford performance nut 
Thats the beauty of it. Ford had DST do it 50 years ago, so there is nothing to try and re-engineer. Crites sells just about everything for it, even headers. And there are plenty of examples out there to look at.
Of course you could go crazy and do a custom front clip, or a full tube chassis car, but the swap can be done without all of that work.