I gotta admit, my mind has been centered on the GX engines, which, being gear timed, you pretty much have to break the block, cam, or crank for them to jump valve timing if it has not been opened. And I still doubt that his engine could have backfired while in storage and lost ignition timing . . . I agree that happens, but the result is typically immediately visible, not months later, and timing shouldn't move simply due to trying to start it . . . unless the flywheel nut is both falling off *and* the key is broken, which was pretty much contradicted when he said it would not come off (the loose nut at least). As long as the flywheel sits on a taper, I doubt the key sees much of the load *if* the torque is correct, acting more as an installation alignment aid, but never say never . . .
But, as noted, I don't do much with the consumer grade Hondas, so they may well have quirks I don't see in a GX series . . .
So, we agree to check most to least likely, easiest to hardest . . .