id go with the 4l65e like tom is saying. my last cruiser i went with the transgo manual valve body kit in a 4l65e and it was great to me.
my new cruiser came with a th350. it lasted about 4hrs of wheeling. If you have any wanting to run a 4 spd now just do it. mock it up for the 4spd now. becuase if you want to change it later it will cost you double to redo everything.