Not so much a miss in the top cylinder as much as the thing doesn't run or kick over.

I'm getting totally frustrated and am not real certain as to what to do next.

I guess I should start asking some dumb arse questions.

How is it that I can begin to trouble shoot?

As far as I can see it the power comes battery to PGM to coil to spark plug.

Am I missing something?

Probably...
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MC28 Track Bike
01' Honda VTR 250 (previously owned)
05' Suzuki Gsx-R 600 (road bike)