The fact that he tapped the CDI box and it's working fine makes me wonder. I had a bad CDI problem with all the classic symptoms - one cylinder not firing, seemed to be heat related. I removed the box and looked at the connector. When they built the bike they had put a tie wrap on the multi-conductor wire going into the connector that was stressing the connector itself. I worked a bit more slack on the wires, cleaned with contact cleaner, and re-connected. It has never acted up in any way since.
I wonder if tapping is moving this connector a little. There shouldn't be anything in the box to come loose but there is some play in the screws that secure it to the bike. You might want to check the connector and make sure there's a bit of slack behind it.
