Did you set the float per the manual? This setting can change pretty often on it's own (gravity), especially during maintenance. MX racers set it EVERY race. It completely changes how the jets interact with the fuel in the bowl. Can really get weird with 2 carbs....Sounds like the carburetor needs cleaning, float set, idle mixture set, and verify stock jetting in the idle, needle, needle jet, and main.
How many turns did you end up on the idle mixture screw to get it idling right? It controls how the bike responds off-idle and returning to idle.