Rest assured, it's not your CDI or coil. Why? The coil fires both plugs at the same time, so your dead cylinder (And your good cylinder for that matter) is getting a spark at BDC and at TDC. (bottom dead center and top dead center) So, if 1 cylinder has spark, both the coil and cdi are still good. That does not rule out a wire problem to the dead cylinder, but if the wire were bad, there would be no spark at all to that side.
Sounds like you have something else going on. Possibly you developed a base gasket leak or a leak around the carbs. Backfires can happen. When they do, you usually lose your reeds on that side. Sounds like you need to tear down the top end to try to identify and rectify the cause. At the least, pull the head off and check out the tops of the pistons.
Let me know what you find.
Gunner
Performance Tech.
Jackson Perofrmance Laboratory