Re: TJ Engine Swap
This might be a good time to look at other engines besides the 4.0 given your setup. While the 4.0 is a great engine, they are becoming harder and harder to find...at least ones with low mileage. You are going to need a doner vehicle that has the engine, tranny, wiring harness and computer. In addition, you are going to need different motor mounts, new exhaust, etc.
As an option, consider a V6 or v8 swap. You will need the same as above, but your choices and available selections are a lot better. I picked up a chevy 5.7L TBI with the 4L60E tranny...harness and all for $500. I would be done now except I got a 'little' carried away and ended up doing a frame up re-store.
I have heard that the Ford 5.0 is about 100lbs lighter than the chevy, and a couple of inches shorter. I know one guy who did the 4.3L V6 swap and has plenty of room. A major factor is what engine you can find for the right price.
In the grand scheme of things, this might be your best short and long term solution. Which ever way you go, I would suggest that you buy the whole vehicle and park it next to your jeep as you do the switch over...that way you can keep going back to it for the misc parts you will need.
Let us know what you do.