Tom,
I'm assuming the bike ran fine before the incident. Since you checked the carbs, lets assume it is electrical for a minute.
1. You changed the CDI unit so it shouldn't be that.
2. It still runs which suggests it is running on one cylinder. If it still runs rough, check to see which exhaust pipe gets hot. Fix the side that's cold.
3. You could have a bad spark plug wire, defective spark plug, loose primary wire connectors or a failing ignition coil which can all cause an engine to run on one cylinder. The coil can be checked by switching the primary and secondary wires between the coils. If the problem switches sides, one coil is pooched.
4. The pickup coil usually causes the engine to completely quit, not run on one cylinder. They can fail when they heat up and open electrically. Then work again when cool.
5. Have you pulled the plugs to see if either are wet, carboned up, cracked etc?
Hope that helps.
