Magna Woes

My cousin has a 94 Magna 750 that the reg/rec recently went out on. It overcharged and swelled up the battery until it basically popped. I've repaired the reg/rec, battery, and checked all the connectors, which were fine, no discoloration, melting, etc. He said right before it shut off it began running poorly and misfiring badly.

Now that it's been fixed, the bike is misfiring. The carbs developed an external leak, so they have received new bowl gaskets, new carb boots (old ones were cracked), fresh fuel and it still misfires. The jets were cleaned when the carbs were out, and when it's misfiring, it'll pop black smoke occasionally, so it seems it's getting plenty of fuel and the adjustments haven't been touched.

The bike ran perfectly before the R/R went out. Is there any chance the high voltage could have messed with the coils or ignition module? It has fresh plugs in it.

I'm just a lot more used to fuel injection, thanks in advance for any ideas.

A defect rr can give very high voltages, so yes the cdi might be damaged.

Okay, broke out the oscilloscope and tested the coils and CDI. They're wiring fine. Coils ohm out fine, but I found an open plug wire. I've got new wires on the way, I'm betting that will take care of it. Why it went out at the same time, I have no clue.