If the CDI was bad, it wouldn't go at all

Actually Scott thats not true. I had an MC16 that ate plugs like they were going out of fashion it also developed a miss-fire on the bottom cylinder. The MC16 actually has 2 x CDI, try swapping these over and see if the problem moves with them in my case it did.

I have documented my experience in the post below

http://nsr250.net/forums/viewtopic.php?t=6434&highlight=
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"............should have bought a Honda"