Your main and pilot jets will affect carb operation all the way down to just cracking the throttle open. The typical carb charts don't show those two circuits having much, if any, affect at that point, but they definitely do on the 350/400 carbs. You mentioned having the top end rebuilt, but did not mention the carbs. With as many miles as your bike has, I would imagine your jets and emulsifier tubes...and emulsifier tube housings need to be cleaned. You'll likely find a fine mud in them with a claylike consistency.
Other things to check are timing, which will cause those exact issues if retarded, and cam chain stretch. A stretched cam chain will not allow the engine to run efficiently with the most noticeable performance issues at lower RPM.
I'd recommend checking timing first (make sure the engine is at the correct idle speed), then cleaning your carbs, and then replacing the cam chain if the problem is not fixed.
Camelman