check your stator output, if it is doing what it should, then the CDI is likely bad. The last ATV I worked on had a primary part of the stator (which went through the CDI for coil excite / spark) then it had a secondary wire from stator to tell the cdi WHEN to connect the primary to the coil.
I used a scope to check all this stuff, but proved it was the CDI.
I do not know if the stators on these bikes are different that that chinese atv i was working on....
If one plug gets spark and the other dont, I would think it is not the CDI unless it has two drivers one for each plug.
2000 Vulcan Drifter 800
Roadhouse classic 2 > 1 exhaust
Okie Smokie intake config
52K miles or so, always going up
Painted flat black winter '12