You probably already checked but you might make sure you don't have any plug wires laying on top of each other. You can get induction firing and that can cause this.
Years ago a friend used zip ties to get his plug wires all together neatly and his engine didn't like it at all. Not realizing what he had done, he tossed a lot of money at solutions before he learned he had caused the trouble trying to make everything look all special.
Heat can cause coils to act oddly, too. Not uncommon to see this.
Have you checked with your oscilloscope again? Usually those control modules either work or they don't (make sure you use thermal grease to mount them). I haven't seen too many work only occasionally. I have seen some Fords go through lots of them before somebody shows up and cleans the mounting area really, really well with acetone and a razor blade. Otherwise they'll sit cocked by about half a mm and if that happens they will get too hot and that will kill them dead.
And finally please be certain you have a really good ground to your engine. HEI requires a good solid connection with ground and if it doesn't get it, you can have intermittent results. I don't think you can have too many ground connections, actually and the old braided cable doesn't really do it for me.
Good luck!
