Whelp, I had somebody come by to look at my bike yesterday so I had to get it running.
Put the carbs back on, rigged up a temp gas tank with a water bottle and some tubing...
And it fired right up on all four cylinders. Sounded nicer than I remember, must have been running on 3 for longer than I'd like to admit. Whoops.
I don't know what did it, must have been something stuck in the carb, because nothing else changed yet. Then, today my new plug boots arrived, so I put them on. They do look nice and shiny.

Thanks for your help guys, I appreciate it.