I just went through the same experience as the OP. My 350 hasn't ran in years - not sure how long, the guy I got it from never got it running...
No spark on the right side (amazed that the bike runs pretty well on one cylinder..). Replaced coil with new - no help. After reading the above, checked battery - it checked at 12.6 volts, so not the issue.
On a whim, I swapped spark plugs, and the right side fired and ran - actually sounded better than the left. So, maybe an easy check will save someone some headaches...
So, I guess I need a set of plugs...