So I'm still pretty novice but to make sure I understand. Your thinking im getting air leaking in where it shouldn't which is causing these concerns? Someone the other day has mentioned as I was leaving the shop that they thought my bike seemed like its running either lean or rich. I'll have to ask him again. He also mentioned that it seemed like one side of my exhaust was getting hotter than the other.
I'm not a carburetor wizard, there are some that have tuned their nose, ears, brains, and hands to master carbs. It's not magic, but it is fluid dynamics and physics which is close.
Running lean means too much air
or too little gas.
Running rich means too much fuel
or too little air.
There are a lot of different conditions that can cause either one. Carburetors are very finicky about how much air and fuel they want.
Fuel has one way to the carbs. Through the floats. Floats are basically the on/off valve for fuel in the carbs, the floats have to float on the fuel at a specific point, otherwise there will be too much or too little fuel. You mentioned duc rebuilt your carbs, they should have set the floats at the recommended level, however checking the float height can't hurt.
The other option is air. Air should only go through the airbox through the carbs. Since the intake operates as a vaccum by design it's relatively easy for air to get sucked in through any openings it can. Another thing to consider is blockages. A dirty air filter or a mouse house in the airbox could give you a rich condition through providing less air then the carbs want.
If one cylinder is running hot it's likely that cylinder is running lean (too much air), if one cylinder is cold it's likely that one is running rich(too much fuel). This isn't a law or anything, just a rule of thumb.