Mine would act very similar to what you're describing, what was happening is that it would run on only one cylinder for a few seconds to a few minutes, always after sitting for a few hours after warming up. One day it just never started hitting the second cylinder, it was finished.
Try revving it a bit and see if that's what it feels like, maybe even listen to each pipe, you can tell when one side has a miss.
Also, feel your headers, the side not firing will be comparatively cool.
The "something breaking loose" could be the second cylinder picking up.
