The choice between rebuilding your engine yourself, having a local mechanic do it for you, or purchasing a long block from a reputable dealer would be based on any number of considerations. I can't accurately assess what's best for you. I'm a "do-it-yourself" kind of guy, so for me the question would be do I have the time and a place to do the work? Can I go without my Jeep for approximately six weeks? Are there any automotive machine shops close to where I'd be doing the work, Etc.?; a good rebuild requires specialized machining. The quick way, and the most expensive way, is to take your Jeep to shop who you can trust to do the job right, whether that be to rebuild the engine or just swap it out for another engine already rebuilt. I mentioned Chrysler as a source for the crate engine. From them, you'd get new everything. You by a rebuild, who knows? If considering a rebuild from "rebuilt jeep-engines.com", or any other source, you need to search for reputation, guarantee, Etc., to get a handle on whether you can trust them. I'm sure there are sources for new Jeep engines that would be cheaper than a local dealer; you need to search. Knowing my skill-level, experience, shop & tool availability, and TIME, I'd rebuild the engine you have, if the block is good, and the head is not cracked. I say replacement 4.0's (re manufactured) advertised in "Essentials For Jeep Vehicles"--I believe the company is Quadratec--with a price range between $1600 and $1800. The engine supplier was listed as ATK, and they offered a 3-year, 60,000 mile warranty.
If your block and head is basically sound, you can rebuild yours for a whole lot less, if you have the time & skill.