The 3.2 does have a 60-degree GM V6 bolt pattern that was only used for auto tranny. The MUA trans for a 3.2 fits the other, larger bolt pattern on the block. The 2.8 tranny would bolt up, but the 3.2's larger-diameter manual trans flywheel won't fit inside of a 2.8 manual tranny's bell housing.
If you converted your Jeep to automatic, you could swap-in the 3.2. Of course the GM 4L30E auto trans is a weak point.
If you can find a 3.2 or 3.5 MUA5 tranny you could conceivably bolt it into your Jeep with more work on mounts & shafts.
'90 3.4 Troop LS;
'89 Troop RS (Exhaust Valve Challenged), now gone to a Good Home!
Yes, I am a Trooper-Holic!!!
Keep On Troopin' !