Any idea if it's missing randomly (any cylinder) or always on the same ones? Trying to rule out the dizzy or the trigger wire going to the CDI or the wire going to the coil.
I'd check every spark plug wires with a stobe light to figure if they are missing randomly or not.
If it's only one or a couple of them with the intermittent problem, you could reindex the dizzy 180 deg and plug the spark plug cables accordingly in the cap. Same one missing? then it's related somewhere in the spark plug wires or the plugs.
You could also test by bypassing the CDI by using a condenser?
To bench test a CDI, check
www.permatune.com
HTH
Marc-Andre