I tested it out today and cylinders 2 and 3 were firing but 1 and 4 were not. A friend came by with his wisdom of CB650s to help me out and we eventually got the bike running decently.
Turns out my pilot jets were clogged again, probably from me using a water bottle to feed the carbs with no filter. Cleaned the pilot jets for carbs 1, 3, and 4 and also cleaned the bowls again. Bike was now easier to start but was still misfiring.
Pulled spark plugs 1 and 4 and they were black and smelt faintly like oil while the spark plug for cylinder 2 looked much better and just a little white on the end of the electrode. My friend cleaned up the spark plugs for cylinder 1 and 4, we put it back together, and the bike is now running much better. Throttle engagement is much smoother, there is a huge power improvement, and first gear put a big smile on my face when I took off.
I installed these spark plugs 3 years ago when I first got the bike but they've barely been used and actually sat on my shelf longer than they were in the engine. I'm guessing 1 and 4 got bad because the cylinders were barely getting enough fuel for good combustion.
I would say I'm 80-90% there now, I only bench synced it so now I'm going to do a little more tweaking to make sure it's all good; I just bought a Digi Sync so I can vacuum sync it soon, double check my valve clearances, double check the timing, and also get new spark plugs again.