Truthfully, if I had a 3-speed C-O-M that fit your 390, why not use it? You're going from one three-speed to another.
The later 390s added an 'extra' motor mount but they are backward compatible.
A word of caution... Ford put 390s in everything including Mustangs. That means it came in a variety of trans mountings. That's why I say, if your C-O-M fits, hey why not use it because all the hookup will fit as well. - Dave