If you just installed a new 250R exhaust, it can smolder for awhile but that doesn't mean that your jetting is incorrect. I tore out the packing and put the spark arrestor on my new R exhaust and the pipe smoldered after the first few runs. I don't know what was on fire but there was some debris that it self cleaned
AS's recommendations are right on...You need to move up to a 42 pilot and a red needle 5th position, that's for sure. You know that pilot controls the low throttle running and the main controls the high RPM running right? I'm not sure you need to go with a 170 main yet...you should be close enough already.
There is a proper procedure on jetting...its impossible to help when we don't know details of your run....all we know is that you ran your bike and it got hot

Were you running full throttle, half throttle, etc? What is your idle set at, etc? Have you adjusted a fuel screw? This is critical to where it is set.