Well lets see, we've got lots in common - so I'll tell you what we've done, that is only what we've done right so far - I'll leave out the mistakes.
We have a 1989 YJ, ours was a one previous owner vehicle so we're luckyier than you on that point. It was a 4.2 with a 5 speed.
My son said to me why aren't you using the Jeep Dad & I replied it needs tires. He said I'll buy you tires Pop & I thought what a good son! A few days later a truck pulls up & unloads five of these Monster truck wheels w/ 33x12.5 Thornbirds. I said to my son "These will never go on that little Jeep" & he said Oh, the lift kit will be here in a day or two! Next day here it comes all new springs, shocks, pitman arm, tie rod ends, wobble stopper - you name it he bought it. A complete 4" lift kit & all the front end stuff! Good thing I'm retired, it took me quite a while to swap all these parts.
A rear axle bearing went bad & we changed it at my buddies garage. We had trouble pressing the new one on - used some heat etc & it went on....... my son was driving along when the rear wheel passed him by going down the road! The axle pulled right out of the housing etc. when that bearing failed & came apart...... lucky nobody got hurt but now the housing was all butchered up where the axle came out. I bought another rear on eBay, I think it was $300 out of a '94 or '95 YJ that was the same ratio. Pretty much the same but this one does have bigger brake shoes. The motor was running like crap, no power trying to turn these big wheels.... the stock carb is a joke so I changed that over to a small Holley (Motorcraft). Starts better & idles but still stinks. Than I hear about this guy who lives down by my oldest son who has a 2004 Wrangler engine, trans, transfer case with less than 15,000 miles on it sitting in his garage for about 3 years! Blood all over it from the accident but its in perfect shape. It came with the complete wiring harness and all the components: starter, alternator, A/C, pullies - belts etc............. The trans is automatic.
I could never have done this swap on my own - all this HiTech stuff now! The motor doesn't even have a distributor anymore! Thank God for my mechanic - my buddy Mike!
It took some time but we got it done.... Had to get a radiator mine was junk when we pulled it out. He had a friend that had a 2000 Wrangler which I bought as a parts car. The radiator from the 2000 was in great shape so we used it. The 89 fuel tank doesn't have a pump in it to supply the increased pressure required by the FI. I won't go thru all the girations that we've gone thru because the new motor specs require 50 pounds of fuel pressure just the end result thus far: I bought a 20 gallon fuel tank from a 94 YJ which has a pump in the tank & puts out like 35 lbs of pressure, we than mounted an external inline pump from a late 80's vintage Big Ford Truck which puts out like 100 lbs of pressure (too much) we than mounted an inline regulator/filter from a '98 Grand Cherokee hopeing that it would bring down the pressure as well as being a filter for the fuel - nah that didn't work! blew right by with a 100 lbs of pressure. Well I bought an adjustable fuel pressure regulator on eBay for about $50 + shipping & that didn't work, sent it back & they sent me another one which won't adjust either. My youngest girls boyfriend is into all these Jap hot rods etc anyway he got me an adjustable regulator that goes for over $400 which has got to let me tweek this puppy to the spec 49.2 pounds +/- 2.0 (ie: 50 lbs) all I need now are the directions on how to hook this thing up, it has all kinds of threaded holes for fittings - what goes where etc.????
But it does run great! I just worry domething is going to blow running this 100 lbs of pressure. If this regulator craps out - I'm going to pull everything off, run just the stock pump in the tank & change the fuel rail to one that has a return line than it should run like any early '90's vintage 4.0
Bottomline: I think you would be better off getting rid of this '89 you have with all these problems take the $5,6,7,8,9,000 you will be putting into it & go buy a later model without all the problems and enjoy!
I've got a Red '97 that I'll sell ya & it comes with a 2000 Red parts vehicle!