2001 2 stroke not running good

Own a 2 stroke 400 4×4. Been pulling hair out trying to get it running good. All my indications point to carburetor but I think I am missing something. Have rebuilt carb and had running decent but not the best. Daughter went on weekend ride and flooded bike in mud hole. Tore down carb cleaned it and now cannot get it to run good. It runs the best with no air filter and no air box cover. If it just put air box cover on with no filter I get very low rpm’s. I keep making adjustments with no luck. I do keep getting a bluish smoke from exhaust no matter what screw adjustments I make.