Keep in mind that carb imbalances are often more noticeable at lower revs. A slight leak at 5% throttle is a greater percentage of the total air/fuel mixture going into the cylinder than at 90% throttle. It's one of the reasons we dont synch carbs at high revs.
Like Monte asked, did you overhaul the carbs or
overhaul them? Often the butterfly shaft o-rings are neglected, and those can leak air. Also, make sure the butterflies are properly installed. They can be put in backwards or installed so as to not seat evenly. Both instances will give you more trouble at low RPM's than higher. Same with the dome cap that you siliconed. If the cap leaks air, the diaphragm won't have the proper vacuum on it and the slide will not lift enough. It doesn't need to be jiggly to leak air, so you might consider gooping up the other one as well. It's also possible that one of your new o-rings was damaged during installation.
One easy way to identify air/exhaust (a bad exhaust leak can also cause you trouble) leaks is to hold a lit cigarette/incense/whatever near various joints (not just the carb boots) and give the engine some revs. Look for a disturbance in the smoke. You can also use the old brake clean/wd-40/starting fluid trick on the intake tract. Spray that stuff at the joints and listen for an rpm change. Usually the engine will bog down and then the revs will gently rise as the spray stuff burns.
Keep a fire extinguisher handy [smiley=thumbup.gif]
Also, confirm that your enrichener (choke) levers are fully returning at the carbs. If the spring is weak or the arm sticky, that can mess up your mixture too. Are they installed correctly?
I'm not sure if installing the discs backwards can mess with the carb balance... hopefully someone who knows can chime inDoes your bike still have the EPA emissions system installed? As Monte asked about the carb vacuum ports... there could be a leak in one of the vacuum lines between a carb and the EPA valve. Also, less likely, one of the EPA pipes to one of the cylinders could be blocked up, have a leak, or have a loose fitting.
Are your plugs, plug ends, and wires the same and in good shape? Sometimes resistor plugs make their way into non resistor boxes. You can verify this with a multimeter. Same with your plug wires/caps. You could try reading the plugs at the most problematic rpm to see if there is an obvious difference in mixture.
Do you have much oil consumption? Are you using good, high octane gasoline?
While my experience has been that motor mount torque makes more difference on the upper rpm vibration (usually around 5K RPM), you could try experimenting with the motor mount torque. 5-10 ft-lbs can make a substantial difference. 55ish front 45ish rear seem to be popular figures
Sorry to go on at length... I just don't want you to give up
