So after enough research to shoot myself, I still haven't found an answer to what's going on with my bike. It's an 03 R6 with about 23k on it.
It started at highway speeds it would blip/surge the throttle like it had bad gas or something. Then it would not stay at idle and die (under ~1500 rpm). It seems like it has a dead spot until it hits above 5k rpm. Every time I pull in the clutch when stopping or slowing down, it will die. I raised the idle, but it still runs like crap between 2k and 6k rpm.
I basically have to keep the rpms above 2k. In the garage I would rev to about 8-9k rpm and let it drop. This would cause a significant flame out the tail pipe and would smell rich.
It has had the coil recall done and I changed the spark plugs this weekend and it didn't seem to fix the issue. I'm planning on taking it in this week unless someone here has a sure fix beforehand?
TIA
UPDATED WITH SOLUTION
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...