Yesterday I was in a friend's shop, and he had a Jeep YJ up on the rack. I did some quick measurements and it looks like the MPFI I-4 might fit the engine compartment. A couple quick calls around uncovered a running '92 2.5L with all of the harness (down to the tail lights) for $300-$400. The earlier, pre-OBDII engines are pretty darn reliable with fewer sensors than the later engines. The engine package is roughly 2' wide by 3' long, similar to the Iron Duke 2.5L.
I think (if it will fit) this would have some of the benefits of both of my previous engine choices (the Iron Duke and the 4.3L). I could pull highway speeds in mountain passes with relative ease, run offroad at angles without flooding, and have a manufacturer-supported engine (there is a ton of support for Jeep engines). I would have to fabricate engine mounts, but that is a minor issue in the scheme of things.
Novak makes a complete kit to adapt the 2.5L to the SM465, which includes the bellhousing, crank position sensor bracket, pressure plate, clutch disc, slave cylinder, pushrod, pivot, and throw-out bearing. It would make for a very clean install.
I really need to get in there and do some more measuring to see if it's possible.