Immobilizer issues?
 

So I just finished my long and tiring drivetrain swap. Got it all buttoned up and full of fluids today and go to start it and it starts right away but then dies immediately. After doing some research and ruling out some of the basics (fuel pump relay, loose battery connections, vacuum leaks) it sounds like it could be the immobilizer? The Jeep in question has the grey key and it suffered an engine fire and I had to swap everything including the wiring harness and PCM from my donor car. From what I have gathered online, it seems that if you try to swap a different PCM in without disabling the immobilizer it will send a fault code to the pcm that was swapped in. Is all hope lost? Can I fully remove the SKIM system and install a new PCM? Can I have the stealership reprogram a PCM so that it works with my current key?

Update: When starting the car, the immobilizer light comes on and stays on after the car dies. It does not flash. Just trying to provide as much info as possible.

No engine light on dash I suspect it's the immobilizer and just krank and no fuel I guess, I want to bypass the immobilizer

Can't bypass it. Or at least not any easy way.
As far as I know, you can't. It's a pain if it plays up.

​​​​The issue is that the we lost the key. Maybe you can have a solution for that

A dealer can program a new key, a Locksmith could possibly program a new key or replace the PCM and ignition. There is no "simple" bypass of the immobilizer.

Yep, you're 100% right about your new computer. When you replace the computer on a SKIM-enabled XJ and you want to bypass it, you need to have the SKIM unplugged (located in your steering column) when you plug the new PCM in, otherwise the new PCM is going to see the SKIM and lock up just like your old one did. If you didn't unplug the SKIM when you put in your new PCM, it's locked now too (it's looking for a programmed key that you don't have).

You have two options now:

1. Get another PCM and make sure the SKIM is unplugged before you plug this computer in. There are companies which re-program PCMs out there, not totally sure if they'd be able to unlock a SKIM-locked one. Doesn't hurt to call around. If you want to try this, I'd recommend WranglerFix. They do XJs too.
2. If you want to keep the SKIM, call your local Chrysler dealer and have them program some new keys using their tool. It's not guaranteed that your dealer will still have someone on staff who knows how to program these, so you won't know until you call. You will need new, blank, chipped keys, and you'll have to get them cut before you head to your dealer. Your Chrysler dealer can plug your VIN into a scanning tool which will spit out a four-digit PIN code which is needed to program new keys. Unfortunately, only a Chrysler dealer can do it, and they might not even be able to since the PCM you have is not the Jeep's original one. Plus, it's probably going to be pretty expensive.

Another good thing to note: If you have two programmed, functional keys, you can program another one using the Customer Learn method, which is explained here (TJ forum but it's the same process for an XJ). If you plan to keep the SKIM, I'd recommend getting at least 3 keys so if one fails you can still program new ones.