A lot of people will advise you to remove the engine and tranny at once. I prefer to do them separately though. I put the engine/trans in my '66 together, but I had to jack up the back end a lot to get it in.
With a 6 cyl., you can cover the engine and probably have enough room to clean/paint everything you want to ....
1966 Mustang Coupe
302 w/ T-5