If you replaced the magneto you would know if the seal is leaking. There would have been oil inside the magneto cover. Also the engine would not run well due to the air (vacuum) leak around the seal. Fast or runaway idle, loss of power, all the symptoms of air getting in somewhere.
Have you taken ohm readings on the mag to determine if it is actually bad?
I'd start there then check your wiring connections carefully. If you're using the kit supplied plug-in connectors, cut them off and solder the wires together and use heat shrink tubing on the soldered connections. Make sure the white and the blue wires cannot come in contact with any metal part of the bike frame or engine.
Let us know what you find.
Tom