Well after a trip to a tuning shop, it looks like they identified my issues.
Turns out the power commander 5 the previous owner installed wasn't installed correctly (Had 1 wire hooked up wrong), but the bigger issue was it was located in the right side panel where it got too hot. So the bike wasn't overheating, but the PC unit was and shutting my bike off when it got hot. I now have a new power commander 6, they relocated it over the battery, and gave it a new a new tune. Now it dynoed right around 180HP and 207ft-lbs of torque (This is at 4,600' elevation, should make more boost around sea level).
More than anything I'm happy to have my rocket back and hopefully have it be reliable now.