OK, IF I understand what you did and what happened.......................please correct me if I'm wrong.
The fact that running a direct line from the battery to the regulator "cured" the problem indicates that you DO have voltage drop in the ignition harness. Visualize in your mind the path (stock wiring)
Battery -- fuse link -- bulkhead connector -- ammeter circuit -- ignition switch connector -- through the switch -- back out the switch connector on dark blue "run" line -- back out the bulkhead connector -- to the ignition system, the regulator "I" terminal, and the alternator field on 70/ later isolated field systems.
well remember i just "fixed my last no charge issue with running a wire from the alt to starter relay stud... there is no fuseable link as the bulkhead is bypassed (alt lead in and out only)
ANY bad connection or drop in this area can cause this surge. In rare cases, surge can be caused by what amounts to R.F. interference from something like a high power ignition system, which can produce noise on the 12V buss and interfere.
only have a MSD street fire box so i dont think its that