Need some opinions on where to go from here...

What intake, carb and distributor? One thing to check is the distributor cap and distributor. 3 & 4 are next to each other on the firing order They don't look like they are firing. 1,8,4,3,6,5,7,2 , That is the only thing that links those two cylinders. If its a dual plain intake they are not on the same runner level so ignition spark ties them together. Cracked Cap?
Holley Strip Dominator single plane with a 780CFM Holley Vac Secondary and a factory electronic distributor. I am almost positive we rechecked all the plug wire routing from the cap to the cylinder, but I will check again, as I am truly hoping it was just something simple and silly like that. I actually thought about buying a new cap, just to eliminate that as well.
I'm no hitrodder but I will take guess that speed master aftermarket heads are aluminum. You can guess they are CNC perfectly flat. My knowing cylinders weren't dressed leads me to think the old cast iron block surfaces weren't dressed either. That begs the question, what head gaskets you're using? Pistons can't swap holes but the horses they make can jump poor fences. Good luck.
The deck surfaces were not dressed by me, but this engine was rebuilt at some point before me, as the cylinders were bored .030" over and the crank was turned .010" on all the journals, so its possible they were done before me. Anything is possible, but it seems like the machine work on the block was done well, and it ran fine before I pulled it apart for upgrades and cleaning. I'm running the thin Mopar head gaskets, I believe either .024" or .028" compressed thickness.