Bet it runs great with the points and MSD. I am diagnosing your problem as EMI (RFI). You haven't mentioned your plug wires. Something is causing the probably more sensitive digital circuits to "see" more trigger events. That is probably interference from the ignition leads finding an unshielded area on the trigger circuit.
I have an electronic device to monitor my heart. Strong fields can be picked up by the leads from device to heart, fooling the device. Same for your system.
