John, your better off taking it apart and cleaning the valves than you are trying to get it to free up with MMO. It's not a big ol' motor that takes hours to tear into.... just pull the heads and valves and clean it up.
As far as it being carb related... it's a single carb on an open manifold. Unless something is blocking the flow in the intake, it can't run good on one cylinder and not the other unless there is a valve issue. (You've eliminated ignition and it sounds like you have tested for intake air leaks.) Time to take it apart bud.
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