I dunno specifically about your bike but, if it's completely stock every attempt should first be made to get it running using the stock components. The air intake system was engineered to match that carburetor. Once you change air intake components to cure a fuel/air mixture problem, you're on your own.. you are essentially redesigning the carb/intake system.
It sounds like the carb was running rich because of air restriction but there are other possibilities. The original problem could be as simple as a too-high float level in the carb. Too much fuel is too easily sucked into the engine.
You added air and improved air:fuel ratio near wide open throttle (WOT) somewhat. However it's still running rich at part throttle. Some system in the carb still has fuel metering problems..
Main jet size controls maximum fuel delivery at WOT.. It has little or no influence at smaller throttle openings.
I recommend restoring the air intake to stock parts and a thorough carb cleaning and adjustment. This bike should run perfectly in 100% stock condition if everything is clean and tight and properly adjusted. Find and fix the underlying rich fuel delivery problem.
Replacing or modifying major parts in an effort to tune a carburetor is not the way to go, imo..