If you have the skills don't let that deter you, it's not THAT bad. All Jurjens's points are mostly valid, but most aren't as difficult as they might sound. You didn't mention whether it was an auto or manual trans Cherokee. If it's a manual then the TCM that is referenced is not a factor, if it was an auto then it becomes an issue of which trans are you intending to use? the TCM is only like 4-5 wires(can't remember without looking) but it's small & easily installed under the dash somewhere. Which trans you have/intend to use will play into the drive line issue, if you are keeping the original eagle trans/t-case then the DL's are no issue(though you will need to modify the bellhousing for a crank-sensor or go to a relocated one on the harmonic balancer), if going to the AW4(if it was auto, if it was manual DON'T use the manual as it will be one of the very week options used at the time) from the XJ then you'll need to lengthen the front & shorten the rear as well as fab some on the cross member. Best solution to the fan issue is to get a few parts from a wrecking yard & maybe a new water pump from the parts store to fit a ZJ Grand cherokee and convert to that belt routing, that'll put the fan back on the waterpump and not off on a seperat idler pully as the XJ started. You shouldn't need to do anything with the dash to make it run, though you will need to do some minor wiring to get the idiot lights to function again. On the exhaust, none of the 4.0 manifolds/headers will connect to the eagle exhaust, and the Eagle manifold won't work on a 4.0, but of all the options you have one of the best as it "should" clear the d-shaft the best. with that said that portion is no worse than all the 4.0 head swap stories out there.
I'm not sure that I've seen a writeup on the full swap either, but I have seen them on all the required components, head/EFI, Trans/T-case. so the information is out there, you may just need to integrate a couple of the swaps that some have done with those that others have done to relate to your situation. I have a 4.0 from a 92(HO/OBD1 injection setup) that will go into the brown Eagle Wagon along with a Wrangler TF999, that should be a mostly bolt in afair other than the wiring for the injection, and as noted that version is a mostly stand-alone wiring harness; I'm also putting together a 4.6 stroked 4.0/4.2 combo that will go into my SX/4 with a GM controller & harness(programmable & tuneable without spending an arm & a leg) I'm going to use the existing T5 in the SX/4 and on nice thing about the GM injection setup is it doesn't require a crank sensor it works off the cam distributor signal.
Skills aside, research & planning are KEY to making it go smoothly & getting it running quickly. Best of luck, I love the 4.0 nice smooth power, reliable & long running for reasonably maintained.