Misfire at cruise, popping/afterfire at 3000RPM

Well I understand you're frustration but you need to work out the problems before you rebuild or you might just be bolting your problems right back on. I didn't have a chance to read all the posts but I do run a six pack and have had similar problems in my ignition. Two things that I would do very first would be make sure that my outboard carbs were working correctly because of leaning problem would be coming into effect around the RPM range you're talking about, but the first thing I would do replace that distributor for another working distributor to see if it eliminates your problems. My guess is it's in the distributor after isolating that you can move on.
Yeah, it’s pretty frustrating. I’m on my second distributor, second coil, two separate ECUs, three different engine harnesses, valve job on the heads. I’ve checked and double checked timing.

One thing AJ suggested was reversed polarity at the distributor pickup, but I don’t understand how that could happen with all those different harnesses and both distributors. I’m not doubting him, I just don’t understand.