You might need a bigger pilot. What size do you have it there? I'm sure you have been through this..but it might be worth another look (from resource page):
4- Adjust air screws (one carb at a time) for highest idle RPM with a warm engine. It will require that idle screw is turned to increase RPM for the cylinder to be adjusted. Air screw adjustment should be made at >2000 rpm. Adjustment should be made in slow, small increments. If air screw is out more than 1 3/4 turns for highest RPM, a smaller pilot jet should be fitted. If air screw is out less than 1 1/4 turns, a larger pilot jet should be fitted. Return idle to normal and repeat for next cylinder. Idle RPM should be 1250-1400 RPM.
The airscrew is a fine-tuning adjustment designed to allow the carburetor to be slightly adjusted for variances in atmospheric conditions. The air screw works with the pilot jet, mainly affecting the engines initial starting, idling and initial power delivery. Proper adjustment of the airscrew can offer direct feed back on pilot jet sizing. When adjusting the air screw, tightening the screw is richer and loosening it is leaner.
If you get no RPM fluctuation when adjusting the air screw there is a good chance that there is something clogging the pilot system or the wrong size pilot jet is installed. In most cases, the pilot jet should be the same as original stock, ref:
http://kawtriple.com/mraxl/carbspec.html Clean the system thoroughly with carb cleaner and blow out with compressed air.
A lean setting will cause your engine to surge at very low RPM’s, bog or cut-out when the throttle is opened quickly and have trouble idling down.
A rich pilot setting will result in hard starting, plug fouling at low RPM’s, sputtering as the throttle is cracked opened.
- Note: Kaw specs for air screw setting is just a starting point. Adjustment is required for best performance.
Each carb must be ADJUSTED for optimum idle. That is done via AIR SCREW adjustment.... seeking the point where idle rpm for that cyl is highest. That is the point where the fuel/air mixture is optimum at idle rpm. Starting from scratch, unless you're extremely lucky, there is no "balance" between cyls or carbs.... one cyl will be pulling the other two. When this condition exists ONLY the carb on the pulling cyl will respond to adjustment. Setting the idle stop to insure that the "pulling" cyl carb is in control of idle rpm will then allow adjustment of that carb to be seen in rpm changes. An alternative is to pull the plugs of the cyls not being adjusted so it would be apparent which cyl is "pulling". If, using this method, an air screw has no effect on idle speed, something is wrong. On a new stock bike setting air screws X number of turns is "close". Changes in altitude, humidity, pipes, or filters and all bets are off.