I have a 2002 450 foreman that I recently changed the motor in. Now the head pipe heats up so hot it glows and when first started up it runs rough when first started until warmed up, if I give it gas it bogs out really bad, other then that the motor seems to run good doesn't smoke at all and no noises in the motor,the air filter and air box lid are missing

 

That is a lean condition. Did it come with the carb? May want to check jetting. If not the jetting then it is sucking air from somewhere.

 

It's definitely lean as mentioned. The first thing you should do is replace the air filter and air box lid because they cause restriction that will help your lean issue. If that doesent completely fix the issue and all your carb boots are tight with no leaks then you probably need a good carb cleaning.

 

Would having the valves adjusted too tight cause this as well?