OK, so I got my bike back from Rocky Mtn this weekend. She is all better and running better than ever. The problem was that the bike had multiple stored codes on the computer. It was showing codes for: tip over, TPS, idle, and misfires. Danny the tech, who is a MRA racer, said that the R6 does not like stored codes and sometimes the computer will go back and try to go into a limp mode.

My advice to others with this problem is to have all your codes and code history cleared first before replacing parts. He said at worst it may be a bad TPS, but after all the codes were cleared, it was working just fine and has been for the last 100 miles so far. The $70 bill was more than worth it to finally figure it out...