Need 4 speed advice

Yes, I would definitely go with the later slip yoke on the tranny output. Not sure what the advatages/disadvantages are vce the flange, but there must be some reason they changed it.

Don't know what the big deal with floor humps is all about. It's just sheet metal or whatever your choice of material, can be fabbed with minimal skills and a correctly positioned hole in the floor. That's how I did it.