Don't you just LOVE IT?!?
I've had a similar issue in the past couple weeks. Took my Warrior in for its first custom map since I've owned it. Been riding on the previous owner's map for the past 3 years, but recently installed a VBAK, so want a new map.
I took it to a shop on Dynotech's approved list of tuning centers. The tech was not able to create a custom map for me. Not a problem -- my issue since my PC3 did not have the 'perfect install', which I didn't realize at the time.
But... they gave my bike back to me with the PC3 not functioning at all! It's dead! Now I have to send it back to Dynotech to have it 're-programmed' in hopes of bringing it back to life. And, in his attempts to figure it all out, the tech RIPPED my TPS wire splice off, leaving me with a damaged wire that I have to now fix. AND there is a scratch in my shiny chrome exhaust. Not to mention that my bike was COVERED in greasy finger prints, from front fender to rear fender (why are they even touching the fenders, right???).
Very frustrating. It's like my worst nightmare -- letting someone else work on my bike and getting it back in worse condition than when I gave it to them. They hooked up the stock ECU just so that I could get home.
Anyway, sorry for your similar troubles. And sorry I don't have ideas on what you should check with your own electrical issues.
Personally, I just wanted to get my bike home and take care of it myself. Really makes me want to never let anyone touch it again. I wish the new PC5 (with auto-tune module) and/or Cobra PowerPro didn't cost $600. I'd love to have that auto-tune feature.
Good luck with your diagnosis, and dealing with the shop.