People have had trouble with the Mopar orange box recently, as they are now made in China. Their silver box is supposidly still good. I don't think that's the problem here though. I'm just curious about the changes you did to your wiring to make this conversion. Is the orange box mounted on the firewall? Long running wires can cause a voltage drop that can dim your spark. I had this issue as some genious put my ignition box on the inner fender on the passenger's side. I'm sorry I can't recommend a spark plug for you here, but the .035 gap sounds good. Do you have a new carb? Maybe it just needs leaned out a bit? As for the voltage regulator, that wouldn't cause your problem either.
Mike
EDIT- If you have a volt meter, I would like to know what you measure between the "+" side of the coil, and ground with the engine running. This is critical, as just one volt can mess you up(ask me how I know). It won't be near 12 volts, but I'll compare it to what I have. This will tell us if your problem is in the plugs/fuel mixture, or the wiring.