Hi John,

I have been restoring MC16 for years now and to begin with it did run rough, very rough.

My steps to success were

1. Clean powervalve assemblies on both cylinders as best you can.
2. Replace float valves as although they may look ok this made no end of difference. Whilst apart set float heights details can be found here for the height.
3. Get some decent spark plugs B9EGS is what im currently using.

I also have recently replaced a CDI unit that was causing me to lose one cylinder once the bike was warm but this is definately not your issue.
Also take a good look in the fuel tank if its rusty as hell your carb bowls probably are full of rust too. I used flowliner to seal my tank before i replaced the float valves and all has been sweet since.

Jimmy