I had similar symptoms. My issue turned out to be a bad connection at the Ballast Resistor. Using a multimeter, check voltages at all the wires pertaining to the ignition system. You could have a poor connection somewhere. Is the motor grounded?
The motor has a new ground wire directly to battery, also the ignition system doesn't has ballast resistor, is directly wired to alternator output
Have someone sit with it idling in gear and try pulling the wires again one at a time and see if that makes a difference.
I'm going to try with car idling in gear and see what happens