I tried to take the carbs out today, that was a miserable fail. I could not for the life of me get to the clamp screw for the front carb. Because of this I could not flip the carbs upside down in the bike. I was able to remove the rear carb bowl, and it was spotless inside. I puled the main jet and it was clean, no varnish anywhere, looked brand new. I couldn't get the pilot jet out because of the angle to get a screwdriver on it, but I shot carb cleaner down through it from the top of the carb and the was no blockage. I could not get the front bowl off though, but based on the condition of the rear I have little reason to think it would be any different.
I pulled the rear spark plug while I had the plastics off, and it looked nice and clean, just a touch of black on the tip. The front plug, on the other hand, was all oily. My new theory is that one of my choke plungers is stuck, causing only the front cylinder to run rich. I put it all back together and it fired right up and will idle with no choke after 30 seconds or so. The idle speed adjuster still has to be turned all the way up to maintain the idle but it does seem to be running nicer off idle.
I'm gonna call a local ATV shop (not dealer) and see what they want to tear the carbs/choke off and try and correct it. I will install a new plug up front though just to be sure. What is everyone paying independent shops to do their carbs, assuming no rebuild is necessary, just a cleaning.