05 yz250f help

I got a 05 yz250f a month ago and the guy i got it from said it was stock yet it has a powerbomb header and a factory 4 fmf pipe, it also has an athena cylinder which from what i understand is for big bore kits... I have not had the bike apart so i dont know if it has the bore kit or not, but my question is, its running really hot, the header is turning orange..., it cools down after a bit of riding but then when you rev it up a blue flame shoots out of the exaust about a foot long, the bike also has a jet kit... Does anyone have any tips to help me get my bike to not run as hot because i really dont wanna melt tthe piston rings... Especially if the bike has a bore kit