I am not real sure what ur asking, but I will try and answer some of ur ?'s as I understand them. '96 and newer Jeeps with the NP 231 have a short Tail Shaft housing/seal so you can take off the rear DS and Slip Yoke and NOT loose any fluid. BUT you should NOT drive too far or ESPECIALLY too fast in 4 Wheel H (AKA front wheel drive) cause the X Case will heat up A LOT! (At least mine did) The Slip Yoke just slides over the splined Tail Shaft and the rubber sleeve is just there to keep mud and dirt off the splines.
I assume you would've researched this before you planned on doing the switch so I probably have misunderstood your questions and didn't provide the answers you were looking for.
You did mentioned "plugging" the rear output Shaft hole
You can't drive without a Rear Output Shaft in because the chain that drives the Front Output Shaft is connected to both Shafts. If your planning on installing the new, shorter, Output Shaft/Housing now and the DS later, you can, but the the caution above (about FWD) still applies.
Hope I didn't screw this post up.
Best, Jack