If it was up to me, I would look into a chev 5.3l engine, and transplant that into you jeep. I am not big on chevy's but their lsx engines made decent power and tq, and are built pretty well. There are quite a few old 5.3l engines in trucks with 300k on the odo..
http://www.novak-adapt.com/knowledge/tj_swap.htmIf you bought a jeep with the d44, you will have 3:73 gears (i think), otherwise you will have 3:07 gears. That gear isnt enough with a stock 4.0l to run anything larger than a 33" tire, and even a 33 is pushing it...and a 33" tire is pretty small in the jeep world. If you plan to build this jeep of yours into a monster, you will be re-gearing shortly which isnt cheap if you dont do it yourself..
Running an engine like the chev 5.3 will help mitigate a gear swap, however your axles will need work sooner than later the larger you go with tires. In calgary, you can get a 5.3 from a wrecker for 1k pretty easily...(and the other dirty little secret is you will improve your fuel economy quite significantly as well).