You might try taking a good look at the coil to the duff cylinder - look in particular at the blades to see if there is any evidence of pitting/charring, as a poor (loose) connection to the female connector of the wiring harness can cause the intermittent sypmtoms you describe. Make sure that connection is clean and snug - mine was just loose enough that sometimes the bike would run fine, and other times go on one cylinder. Drove me completely nuts as I had this going on with both cylinders intermittently. When I finally thought to replace the female connectors with new ones, problem solved. Hope that helps.
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-Jim
'93 MC21