Got a break from the rain this morning and rigged up the 3ohm dyna mini coils that came with this ignition. I just zip tied them together through the frame for a test rather than worry about mounting them properly. All four cylinders were firing with points, so I went ahead and installed and timed the Charlie's ignition for what feels like the 12th time. Seemed to be working, so I took it for a spin and bingo, must have been something up with the 1-4 stock coil. Curious why the 1-4 coil would work at idle but cut out under load if anyone can explain it to me. It read 4.7ohms between the posts.
No backfire or stutter with the dynas but I still don't have much power above 6k rpm. I'm thinking that's either due to jetting, or the 34 tooth rear sprocket the PO put on lowering the power band.
After reading many threads on coil resistance and ignition systems, I probably won't stick with this set up. I have a Hondaman ignition on the way, so I'll probably run that once I figure out what do about the coils.