Forgive me for coming into this half way through, but this almost sounds as if you may have some Neutral Safety switch issues? Given that it will cut out intermittently, and runs when shifted into neutral, and that it happens with or with out the Pertronix unit?

Just a quick guess, and not knowing the whole story... but it may be worth looking into? That could cause some problems?

Good luck - Brett - 67 Drop Top 455!