I would definitely dump the AX15, as they are a very weak tranny. It probably wouldn't last long behind the torque of the diesel. An NVG3550 would be a better alternative, also found in later model Wranglers.
I don't have any idea about the bellhousing issues, though.
Cool swap!
Casey
1995 K1500 Tahoe 2 door, 6.5LTD, 4L80E, NP241, 3.42's, 285/75R16 BFG K02's; 1997 506 block; Kennedy OPS harness, gauges, Quick Heat plugs, and TD-Max chip; Dtech FSD on FSD Cooler; vacuum pump deleted, HX35 turbo, Turbo Master, 3.5" Kennedy exhaust, F code intake; dual t/stats, HO water pump, Champion radiator; Racor fuel filter