So I just took the carbs off to take pictures, everything looked good, slides looked pretty even, jets all the same, then I started looking at the wires and I realized that if I stretched them to the limits I could swap 1/4 and 2/3, so I excitedly put the carbs back on to test swapping wires.
With the wires swapped, the bike didn't even start. I put the wires back where they go and started it up, ran fine. I started taking a video and pulling plug caps one by one to see the idle change when they were pulled. Pulling 1 or 4 killed the engine, then pulling 3 just dropped the idle but didn't kill the engine, then I pulled 2 and the idle actually dropped unlike every test before. So it seems all the were firing.
I put the air filters back on and hooked up the carb sync tool and did another carb sync. This time I had to raise the rpm to around 2500 for a steady idle because some cylinders still fluctuated too much like before, so I kept the idle higher for the sync. They were not perfect when I started so I had to make some small adjustments, I could hear the idle changing everytime I adjusted an individual carb. I got them all close and put it back together.
Bike seems to run pretty good now it doesn't have as much power around the high range, about 3/4 throttle and is still a little poppy with the d7ea plugs, but overall runs better than before. I am not sure why they are all firing right now.
I think i need to richen it up over all by adjusting the needle clip settings.
I still don't feel comfortable that out of nowhere it's firing again, I'd like to upgrade the ignition in the future still. I will update this again if this problem persists, about to go for a long ride!
Thanks everybody for the help.