LM7 5300 swap into Jeep Wrangler

I bought a Jeep Wrangler with an LM7 5300 GM engine swap and I have an intermittent issue.
CURRENT ISSUE: Most of the time no start (no fuel, I believe this is a SKIM issue).
HISTORY: Ran fine when I got it but wiring quickly became a mess and I had to fix a bunch of shorts, ground, etc and removed the alarm which was causing issues.
This is when the SKIM issue started, I read into VCM editor, enabled SKIM and wrote it. The engine ran great, Finished fixing wiring issues and drove it around a while (maybe 40 miles).
Now it's having the issue again, I went to delete the SKIM and when I read into VCM editor The vehicle pulled up as a GM5.3 with a different VIN instead of the Jeep Wrangler and the correct Jeep VIN. Also all different tuning options under every category but not SKIM and VAT is disabled (also I don't have a license for this GM VIN).
Every now and then when I leave the battery disconnected and reconnect it, the Jeep will run fine.
Maybe I fixed something in the wiring and now it's reading from the GM5.2 PCM for the engine and not the Jeep Wrangler ECU?

I am thinking I will try tomorrow to see if I can't just unplug the GM PCM and then read/write the Jeep with the SKIM disabled.
Are there any other recommendations that I might be able to try.

On top of it, there is a Crankshaft Position Sensor correcting unit wiring into the Jeep ECU. It seems excessive to have a Jeep ECU, GM PCM and a CPS unit, it's there a more simple option?

I'm not sure how much help you are going to find for this Frankenstein. Without a wiring diagram of everything, we can't tell what is controlling what.

What era Wrangler are we talking about? The easiest way to make this work would be to make it function like a "hot rod" setup with a standalone setup, either aftermarket or GM, but you may lose a lot of function such as gauges if this is anything like a newer Jeep. And it probably is since you keep talking about "SKIM", whatever that is.

@gtstory - thanks for the reply, I will keep that in mind but I'd hate to have to redesign everything. Its a 2004 wrangler 2dr Rubicon.
The SKIM is the key security cut-off that reads your key and checks the computer to make sure it's a key that is programmed.
So I did unplug the GM PCM and reprogrammed the Jeep ECU with the SKIM and VATS disabled.
It started a few times then didn't.
I let it sit overnight and went at it again today and it started dozens of times with no problems and ran fine all day.
It does still have the key light in the gauge cluster on and I even tried plugging the key reader back in (The SKIM disabling instructions said to unplug it after programming the ECU). Everything is still running fine.

What a goofy vehicle.
I'm hoping I am done with this strange issue for now but will try and figure out the key light on the gauge cluster.