The first thing I did the other day when it started to run like crap was change the plugs with new iridiums and the symptoms did not change. We plugged off the exhaust valves and it ran better, but by no means alright. Next was checking and cleaning the power valves, a bit of carbon build up but expected at 850 miles. Swapped out a solenoid, since I had a spare sled to change it easily enough.
Today we had an identical sled and swapped ECUs, no change in symptoms. We put my plugs in the other sled and it ran fine, then put the other sled's plugs in mine and it ran right. I can't explain how my sled would run like crap with a set of plugs, but be fine in another sled. Pisses me off as this was the very first thing we changed the other day and it didn't fix the issue until yet another set of plugs was installed.
Thanks to Cory Boston and Next Level Power Sports for helping me get it figured out.