Short beds are definitely the way to go if you really want to wheel it. Kinda wish I started with a short bed but I couldn't pass up the deal on mine. Swapping a newer style drive train into an '86 is a good bit of work. I've heard mixed things on if you need to massage the firewall to make it fit. From look at my '92 and '86, it really does look you have to. The front radiator for the 4.0L is not a straight bolt in either. You will need to make some brackets and do some clearancing on the frame to get that in there (I chopped the hell out of mine to get that rad in there). You will need basically everything from a donor (drive train plus complete wiring). You might also need to get your drive shaft cut down since the '86's have the longest of all the Comanche drive shafts for a 4wd equipped one.
[B]1986 Jeep Comanche 126000+ miles[/B]
Long Bed, Chevy 350 TPI (5.7L V8), AX15, NP231
Roll Bar, 15/38.5R16.5 Ground Hawgs, Bastard lift (Custom 3-link long arm system, 4.5" Rusty's front springs w/ 1.75" spacers and 6.5" RC shocks, SOA rear), Dana 60HP/Sterling 10.25, 4.10's, Recessed winch, more mods to come...
[B]1992 Jeep Comanche 174000+ miles[/B]
Short Bed, 4.0L I6 HO, AX15, NP231
In the process of doing a frame up restoration.
[B]1990 Jeep Cherokee XJ 207774 miles[/B]
4.0L I6, AW4, NP231. Tom Woods SYE and Drive Shaft, Rusty's 8.0" Long Arm Suspension Lift, 36/13.5R15 Super Swamper IROK's, Dana 30 Front, Tube Diff Guard, Dana 44 Rear, 4.56 gears, Ox Locker, disc brake conversion