This is all based on my experience with other engines, and I am sure I will be corrected if I'm wrong, but as far as I know, there are no splines of any kind directly between the engine and the transmission. The manual has splines to the clutch, and the auto has splines to the torque converter. The clutch pressure plate bolts to the flywheel, the torque covnerter to a flex plate. Since you will swap the flywheel with the manual, I would guess the only thing you would need is a pilot bearing (bushing?), and I dont know, but I would guess that that is as simple as getting one and putting it in the exisitng empty hole in the crank.
Travis