I have my red 12v feed for my MSD hooked to the ballast resistor with the dual-wire lead/plug. I had problems just like this. I thought I had a good 12v source ( which I did ), but with the key in IGN2 when cranking, the 12v was interrupted on the single wire side of the ballast. So, I swapped it around after some mentoring here on moparts and voila, it worked. I too have replaced the coil resistor of the ballast resistor with a straight gauge-appropriate wire, 12v in, 12v out.......

Attached is a picture of the engine bay, you'll see where my 12v feed it placed on the one side of the ballast resistor. I just used a "T" adaptor.