Hmm....hate to say this this way but something seems odd about running fine all those miles and then putting on a pipe and PCIII and hitting the dyno and a subsequent failure.
Sounds like there might be a lean spot in the PCIII calibration that may have caused burnt valves...???...or even a holed piston. I would suspect a burnt valve rather than a piston/ring problem but never say never.
That is one of the problems with doing tuning work on a high specific output engine like the FJR has. They are typically not very forgiving of beging run hard with a fuel injection calibration that is slightly off. And if it was "tuned" on a dyno for max output then it is even more scary because what makes nice dyno numbers is typically too lean for day to day operation and hammering on it repeatedly....or running for periods of continous WOT. Easy to burn a valve due to high exhaust temps and/or get into detonation from too lean a mixture and/or induce preignition via plugs that are too hot for the (now) too lean A/F ratio and/or get into detonation induced preignition from leaness under heavy load.
I suspect that there is a correlation between the pipe/PCIII/dyno tuning and the loss of compession and high leak down rates.
I think Jestal hit the nail on the head.
At about 93k miles I had Montclair Yamaha check the valves and put in a new Cam Chain Tentioner.
The valves still didn't need adjusting, but when I got the bike back home it was running real bad.
I bring it back to the shop and they can't find anything wrong with it. So I bring it back to Lou at L&L motorsports to see if it was the PC, it wasn't but he did LEAN it out to make it run better.
I bring it back to the dealer and after a big hassel, they agree to check the cam timing and sure enough it was off. They adjusted it and the bike ran fine.
I never brought the bike back to L&L to have the PC retuned.
My fault.
Live and learn.