OK, so everything I would do, you were doing and each paragraph built to some good troubleshooting.
Without being there, here is what I think I recommend, but it's a bit of a guess.
1 - Use a piston stop and make sure your balancer is right. It doesn't seem like a problem, but if it is spinning like a sheared key, may as well verify TDC the correct way and rule it out
2 - I would probably get to every plug wire with an Ohmmeter and visually inspect the crimps to make sure there aren't some damaged or broken
3 - Verify you have a good path to ground, both for engine and for body, just to rule anything goofy out
4 - Just a note, you ended up getting it to idle at 600, which seems low enough with that cam in a little engine, but just a point, in a 4 corner idle carb, 3/4 out is about perfect, so although 2 corners typically end up at 1 1/8 or so, that's about where I see 4 corner
So I don't have an answer but...if the balancer isn't spinning free, you don't have some intermittent firing and cross firing, we'll have to think some more