does it have a low oil shutdown?
I would say the low oil shutdown switch might be malfunctioning, but since it was ran low on oil it probably doesn't have one... Have you tried running it with the kill wire unhooked? That would eliminate any ground issues causing intermittent spark possibly
there was another guy awhile back that when he pulled his spark plug out, and checked for spark, it sparked, but the engine wouldn't start, he unplugged the coil kill wire and it ran, but blew up! The low oil switch was preventing it from running.
I'll do some more thinking.....