I was not available on the ihon forum yesterday charles, I had a binder u. Student here and I'm inna massive crunch trying to get a transmission conversion system built/assembled and delivered to an ihon customer by noon on Monday 125 miles away.
In the future, if you or any ihon customer has an issue with any work which we perform, please...contact us directly so that we May work you through whatever is going on. I personally am the only person who knows your system and distributor, this is not run-of-the-mill stuff and is a one-off system for your vehicle even though it's certainly not out of the ordinary. Had you called me, I would have talked you through this and saved alot of trouble and conjecture.
Your first issue was that you initially did not install the distributor back into the engine in the correct position. Due to the design of the delco distributor and the engine peripherals, it will correctly install in only one exact location/spot on an I-4 engine. The delco cap (and no other distributor cap) cannot be "re-indexed" due to the method of hold-down, the window location, and the key for the cap/body interface.
Random high energy spark "leakage" is very common when incorporating any cd ignition box, that system can pump in excess of 40kv at 100+ millijoules. You must use a high quality cap/rotor and plug cables to direct the spark to the plug gap and not the nearest ground point.
The pertronix conversion is "common" for all delco distributors which use the externally-adjustable breaker point set. However, there are detail differences in both the module and the magnet ring for specifc applications. And over the years pertronix has changed the magnet ring for the delco unit. Even though it has eight magnet segments, only four are actually magnets and those four must be properly phased at the point of manufacture.
On two previous occasions, I have found very similar issues to yours when using a p-tron in an I-4 delco. But neither were triggering a msd box so the situation was easily resolved. The msd changes everything. Pertronix simply packaged the wrong magnet ring in the wrong package. I have no doubt that is what the secondary issue you are experiencing now is.
I have two more I-4 application pertronix kits on the way to me right now. As soon as they arrive, one will be installed in a fresh delco distributor that is identical to the one I just completed for you and I will send it on. But you have said that right now the engine is running and drivable, continue to do so until another replacement distributor arrives. Once you have swapped it out again, I need that distributor you have now returned, I will reimburse you for the shipping personally, not ihon. The pertronix units we use are not sourced from pertronix, I must have the faulty part so that I can address this with the distributor for these items, not pertronix.
The setup of the magnet ring shimming and mounting of the module is unique in each of these delco type distributors, the module itself varies greatly as to the exact position it's riveted to the mounting plate. So we don't just slam these parts into the distributor nor can you indiscriminately swap parts around. The setup is a bit more tedious than encountered with Holley, motorcraft, chrysler, etc. Distributors. Had you attempted to install a p-tron in your distributor before rebuilding, there is no way that the magnet ring and module relationship could have been correctly achieved and it would have failed immediately due to a collision between the two parts.
Your distributor was damaged in the past by someone beating on the mechanical advance components with a hammer or something. I had to repair all the damage and replace the counterweights and the incorrect springs that had been installed also.
The distributor cap I see in your pic is filthy, as was the inside of your distributor when I received it (looked like it had been dropped in sand). I suspect that cap has a microscopic crack in it (very common) and the msd box hugely magnifies the effects of a cracked cap. Replace it with new.