Start inspecting your ignition, coils, and plugs. Are there any loose wires? Anything grounding out intermittently? Have you verified it's idling on all 4 cylinders?
Your fuel looks fine, so move on if you are confident the carbs are now clean. (You could double check quickly whether clear tube level is still where you left it).
Confident they're clean. I didn't soak them in anything or use an ultrasonic cleaner but I'm confident. I will check clear tube in a bit once the tank goes back on.
One thing that I don't think is related but I might as well be transparent, my headlight low beam filament has been blowing. Twice so far when out for rides about half an hour in length with a lot of revving. But it has happened and the bike's performance hasn't been affected at all until a couple days ago. I got a new headlight bucket and omitted the grounds to the bolts where the headlight gets mounted to the forks. I thought the main ground was good enough but I guess it's not. I put them back on and tested for continuity and it's a good ground. Haven't been able to test if my low beam blows or not since this stuttering started happening. Will check ignition. Is there a way to test condensers? Other than swapping?
I'm reading through this post:
http://forums.sohc4.net/index.php?topic=89297.0 I don't think he was having the stuttering symptom, though.
When I came home the night this started acting up, the #1 header was hot. 2-3 were warm but I could hold my finger there without getting burned. #4 was...I don't really remember. I think it wasn't that hot. When I went out for the ride yesterday after the carb cleaning, it seemed like all 4 were hot after I started it. I don't remember testing the headers after I came back from the ride, though. So not sure it's idling on 4 cylinders.