SO, I knocked out a few things on my list this weekend. Not as much as I wanted, but here's what I did (in no particular order):

I double checked the grounds under the orange box- no change.

I swapped the orange box with a cheap parts store replacement- no change.

I currently have it timed at 20* initial and 35* total. I tried 10*, 15*, and 25* initial- no change

I put a timing light on each plug wire and brought up the rpms until it starting popping. I couldn't find the cylinder with an inconsistent flash. I even did this in the evening and couldn't find anything.

I ran the car at night to check for shorts along the plug wires. I actually saw one flash one time. It looked to come from either the 1 or 3 cylinder near the plug. This only happened once and I could not duplicate it, even though the popping persisted around 1,800 rpm.

I forgot I loaned out my multimeter, so I wasn't able to ohm the plug wires. I plan on borrowing one from my neighbor today or tomorrow to check those.

Still need to check rotor phasing as well.

Something I did notice was that sometimes when it pops, it'll start the starter spinning. And sometimes the starter will make a loud shreaking sound. Not sure what all that is about...

I was able to get a video of the popping. Hopefully this shows up. The quality is bad but you can hear the popping as I bring up the rpms.