Foreman bogs/stutters from idle to WOT

My 01 foreman 450 ES is bogging down/stuttering (and sometimes afterfires) in 1st and 2nd from a standstill (idle) to WOT. But the problem can not be duplicated in nuetral. There is no problem when i advance the throttle slowly. The problem started about a month ago and since then i have been tinkering, but with no results. The air filter is clean, carb is clean, and new spark plug. I have not checked the fuel lines or fuel filter or pump. I have played with the idle screw and at a higher rpm it seems to fix the problem but then the rpm is to high to get it to downshift. The foreman is stock except for a K&N air filter and mud lites. Originally i thought it was bad gas (water) but since then i have put two tanks through. I don't know what the culprit is and what to check next.