1965 A body 4 speed ball and trunion to Slip yoke ?

You can do it either way. With or without the ball and trunnion. Considering the transmission mods, I'd leave it ball and trunnion. Then you'll only have to essentially change one end of the drive shaft and not mess with the transmission at all. Just one peon's opinion.
So i can make the rear end side a slip yoke and leave the transmission side ball and trunion?