Ballast resitor

First a proper functioning charging system should have your voltage at 13.8 to 14.1 volts. Nominal voltage on a fully charged battery is 12.8 volts. You said 13 but if it's 13.0 then that is low but would not be the reason for your misfire.

What are saying is starting to point at the MSD box. I missed that you were using a dual point distributor. I don't know how two sets of points would effect the MSD but I would be inclined to remove one st of points. It's not going to do anything positive and it may be impacting the MSD.