From caferacer.net: http://www.caferacer.net/forums/topic.asp?TOPIC_ID=11580:
Tuning a carb is far more than just changing out a jet. Your first step is to ensure the engine runs well at full bore - that's when the jet is in full flow. You do this by putting in a new set of plugs and run the bike up to full throttle (on the road). Cut the ignition and check the burn color on the plugs - if they are a nice light brown and your bike is running good at full throttle then the jet size is correct. Your next step is to determine how the bike runs at 1/4, 1/2 and 3/4 throttle. These settings are adjusted by moving the jet needle up or down depending on the reaction of the engine. When the needle is moved down, it leans the bike out - when moved up it will richen up the mixture. This tuning step is used to adjust the mid-range of the carb. In most cases there is a little give and take when adjusting the mid-range.
Finally - there is the idle adjustment setting. This is done be adjusting the idle air screw. Typical setting is 1 and 1/8th turn out from the air screwed all the way in. On some bikes there is an additional idle screw that is used to set the carb idle. In a multi carb setup (2~6), carb sync gauges should be used to sync the carbs to each other. Again the air screw and/or the cable is adjusted so each carb provides the proper amount of gas for all throttle settings.
Bikes that stumble a little during fast throttle cracking is usually cased by the mid-range not set up correctly. Engines popping is usually a combination of valve, ignition and carb adjustment settings. Valve timing is easy - just set them up as called for by the manual. Ignition timing again is an easy setup. Carb tuning is done in the order of full jet operation, mid-range and finally idle settings.
Strictly referring to a chart to pick a jet size will only get you into a ball park. You still must do a plug reading to determine if you have selected the proper size jet. Things like state of your engine (beat or new), density altitude, what kind of pipe and air filter you use will determine your jet size selection. Charts are useful to getting your close - you still must tune for good performance.
From your description - it difficult to tell you if you have the proper jetting. Try checking the plug burn at full throttle and move on to mid-range adjustment. Your valve and ignition timing should be checked and adjusted before you start messing with the carbs. Remember to ONLY change one item at a time and check for improvement.
Take your time, follow your manual and you should have good results.