This is follow up to a question I posted a couple of months ago but can't get to anymore for some reason, and google doesn't allow you to respond on an old thread.
Found Here:
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Ok guys thanks for all your help, but the problem came down to the computer. I bought the engine, wiring harness, and computer from a salvage yard and was told that I was given an engine from a 94 YJ no problem right? Well after pulling many hairs we went and got a book on the Grand Cherokee (we had a hunch) from a friend and were able to identify the wiring harness and computer as a Grand Cherokee's by the color codes on the wires. The Grand Cherokee has that security lock system which of course my Jeep does not, so the computer was turning off the system because it could not find the key's chip. Very frustrating. I called the salvage yard and was less than diplomatic but I got the right computer (I found it myself) for no additional charge, and now my YJ runs quite well. So once again thanks.
Oh and for anyone considering a 4.2L to 4.0L swap, DO IT! However save yourself some headaches and just figure on getting the swap kit from Hesco. I was trying to be cheap and it ending costing me a lot of time I could have been four wheeling. The price isn't really that bad and they are EXTREMELY helpfull.
Mike