65 904 vs 66-up 904 differences/advantages?

As you noted, your current dual cable operated 904 has a rear pump,which allows the car to be push started - not used in 66/later 904/727s. It also has a large rear bearing to help support that pump (also not used in later ones); it's a ruggedly built transmission in of itself. Against: it's dual cable operated, one for park and the other for forward/reverse and has that ball & trunnion flange. A 66/up to when they changed to a spool-type transmission mount V8 904 should bolt right in with minimum, if any, mods to the transmission crossmember. As you noted you lose the shifter and must convert to the later shifting mechanism. There was a company who made a conversion kit to use a later transmission with your original shifter but believe they have gone belly up. I'm sure others will add more info.