LS Swap Without Deleting VATs or Reprogramming PCM

Hey all,

This is my first LS swap, so I'm doing my best to learn everything. I'm working on a 5.3 swap into my 2003 Jeep Wrangler. I spent some time on the phone with an emissions technician and he basically told me that Colorado now checks the PCM and if it's been reprogrammed at all, it's an instant fail. Unfortunately, if I can't get this build to pass, I'm just building it to sell to someone who lives further away from the city than I do.

My current thought is pull a junkyard PCM and BCM from the same vehicle, then get the key/chip reprogrammed by GM so that it matches the BCM code and tells the PCM everything is good.

Would this work?
Are there easier ways to get an LS swap to run without reprogramming the PCM?
The goal is to run the GM PCM on everything engine related, and then the Jeep PCM on all the non engine components; would there be any issues running a stock GM PCM without any of non engine components connected and not deleted from the computer.

I also was reading about bypassing the VATs by plugging the PCM into another GM vehicle and running it for a bit several times. Does bypassing the VATs change the programming at all or would the computer image still be stock?
Would bypassing the VATs work for what I'm trying to do?

Thanks for the help!