What leads me to believe that it may be an issue with the spark advancer is that - and correct me if I am wrong - it is the only component from the beginning of the ignition system chain that controls the two circuits leading to the cylinder groups, hence the alternating of intermittent failure of each cylinder. Thoughts?
The 650's spark advancer is largely 'fixed' in position due to Honda's attempts to meet the egregious DOT/EPA regulations contrived against Honda in the late 1970s. So, they don't provide adjustment: you only get to check it for malfunction.
That said: the spark advancer itself can (if messed with too much by someone) end up with some looseness in its operation that can cause erratic spark timing. The little lobe (they call it a 'cam') on the head of the advancer, which has the trigger 'bump' on it to fire the spark, has been found a bit loose from time to time from what I've read, though I wasn't there. So, check the advancer for things like too-soft springs (this will appear as reaching full advancer before 2250 RPM), which will cause erratic timing shift back-and-forth until higher RPM (like 3000+ RPM) when viewed under a timing light. If that happens then the springs may need to be trimmed back a little (start with 1/2 turn) to hold the advancer's weights steady. While you're there, make sure the advancer weights have not wallowed out their holes on their pivots: this makes for 'jumpy' timing when viewed with the strobe light, until the full advance is reached. Usually snugging up the springs will minimize this bug, too.
When the timing signal starts becoming too irregular the little CDI amplifiers cannot response fast enough to keep up with it, and they will not fire as the result. They have a built-in time constant that does the fast-charge fire of the coils, and it needs to be relatively regular versus RPM in order to work smoothly. If the timing marks jump around under a strobe light, this is the cause.
