If the coil is making proper voltage, the problem has to be after the coil - check the plug wire, cap, and spark plug itself. You can get little plug wire testers at auto parts stores for a couple dollars that should do the job. Another thought: the coil may have been grounded through your body when you held it, but not getting a good ground when it's mounted on the frame, so make sure the ground is clean. Good luck!
PS Not sure the exact spec. for plug gap on the CT90. My XL100 (77 model ) uses .020" and works well.