PCM Woes
 

I got a Check Engine Light driving down Loveland Pass last weekend. It went off after I got back home. Went to O'Rileys and they found a P0107 code using a Bosch scanner. After a bit of research, I found that there is a TSB (18-08-00) for that code when you decelerate at high altitudes: http://dodgeram.info/tsb/2000/18-08-00.htm . Basically a PCM flash fixes it and mine hadn't been updated.

I do a lot of mountain driving so I figured it would be best to fix so if the CEL is on I know it's actually a problem instead of getting used to it being on all the time. I assumed that only a dealer can flash the PCM so I took it in. My first dealer service experience.

Today I got the call that they want to replace the PCM and the Transmission Control Module. Minimum $1000 for the PCM and they can't find a Transmission Control Module but probably similar. According to the service guy they couldn't access the PCM with their equipment. I nodded and drove away after paying a $135 diagnostic fee. The CEL is on again.

This sounds quite a bit fishy to me. Besides the fact I could probably buy a whole parts XJ for $1k and think I could get a used PCM for <$100, I have a few questions:

1) Does a PCM update need to happen at a dealer, or can other shops do it? I would rather not go back to a different dealer for a second opinion on getting the update and pay another huge diagnostic fee if I could do it elsewhere.
2) As far as I can tell the jeep runs and shifts fine. There was only the one code when I had it looked at it at Autozone. That doesn't seem like a failed PCM. Are there connectors to the PCM that could be bad that the dealer didn't notice when they were hooking up their tools? Any test procedures I could run myself? I'm no electronics servicing expert but could borrow a scope from work.
3) More of a Colorado specific question, but if I replace the PCM and Transmission Control Unit with junkyard parts, will I need to go back to the dealer to get the correct VIN and mileage programmed into it to pass emissions, or can I just bolt on and keep driving?