Just thought that I'd finish my tale....
I got the bike back after it's second visit, and it's running well. I haven't put the PCIII back in as yet so it's popping and farting like an ole timer.
I have some tune adjusting to do, but she pulls like a MACK truck.
All in all, I'm pleased with the experience. The Service Manager, John, was awesome about the whole thing.
What happened is that they didn't disconnect the PCIII and test their work. In addition, their diag-tool decided to take a dump at the same time. If their diag-tool had worked they would have realized that there wasn't any vaccuum and so the bike was running super rich and fouled the plugs. Once John figured out the problem, replaced the plugs at no charge either, she ran like a champ.