I had similar issues trying to install the petronix 1665A into my '69 with the stock coil. I had a small miss in the ignition and couldn't track it down. Tried starting it several times and wasn't getting any spark. I made sure I was never leaving the ignition in the on position for more than a few seconds. Double checked all the wiring and polarity and all looked good. On about the 4th or 5th time turning it over, I started smelling something burning. Quickly pulled the battery cable, and the petronix had burned out.
Decided to get the flame thrower coil and bought a 2nd 1665A. Still wasn't getting any spark, but no smoke either. I was really close to giving up and going back to points, but decided to try the petronix II 91665A. Note: when I took off the 2nd petronix 1665A, I could see a small burn mark on the side.
Made a short prayer and tried turning it over. I was definitely getting spark now (yay!), but it wouldn't actually start (lots of spit and sputter). Found TDC on #1 and rechecked all the plug wire ordering and all looked good. Loosened up the dizzy and decided to try giving it small twists. Tried turning it over again and BOOM, she came back to life. Put the timing light on and made a few tweaks to the dizzy and she was purring nicely and the miss was gone.
Took her out for a spin and she definitely had more pep and ran smoother than she ever had since the frame off resto. It's only a 3 speed, but it ran smoothly at 60mph @2800 RPM. I'm glad I stuck with it and the petronix II 91665A and flame thrower combo worked nicely for me. Just passing along some of the frustration and solutions I ran into in case others run into the same situation.