There was either some other defect that caused the accelerated valve wear (which could still have happened in the 26k miles between checks) or the cause is something else other than valve clearances.
which routine checkups and early diagnosis may catch before it progresses too far to treat. -- your family Dr.
Carbonized valves not fully closing leading to death via heat and recession?
I think I'd go with these two comments. Random sudden valve problem in one cylinder would seem to be explained by the carbon deposits issue -- and this would hardly be the first time an FJR had problems with carbon deposits.
But I believe another point (about riding an ailing FJR) is implicit in both comments. Mike rode across the Nevada desert during the day on a hot day with the problem in evidence. That went on for several hundred (or more) miles. As ionbeam pointed out in post no.40, once you start having a heat created problem with valve seating, the erosion of seat and valve surface gets progressively worse fairly quickly.
Everything about this, from the missed valve clearance inspection to the possibility that carbon deposits prevented valves in the non-firing cylinder from closing, is compounded by this bike having been run in that condition, in the heat, until the seat-valve erosion was so bad that there was no combustion in that cylinder anymore. It's easier to get away with that sort of thing in an old VW than in a Ferrari, and this engine is closer to that of a Ferrari.
So, on top of the point that Bounce made earlier about this thread being a perfect example of why the maintenance schedule must be observed, maybe we should note that it's also a perfect example of why you don't run a bike that is limping any longer than is absolutely necessary to get it repaired. By the time this bike got to 'Zilla's mechanic, most, if not all the damage was already done. When Zac's guys get it apart, they're not going to see an engine that had just started missing (probably initially due to carbon deposits), they're going to see an engine that was hammered way past the time it started missing until the affected cylinder wouldn't run anymore. Maybe the initial carbon deposits are still there. Maybe they burned off around the time that the seats and valve surfaces had burned so far past spec that the resulting heat problem was in the accelerated damage phase.
Next time, truck the thing home in a U-Haul, have it carted to the nearest dealer, do anything other than limp it for hundreds or thousands of miles.
Really sorry you gotta go through this, Mike, but I'm glad you're on the way to getting your bike back with the problems fixed. Besides, we never learn a lesson well enough until it's learned the hard way. Hope you're riding again soon.