Stock carb, ...stock bore, stroke,head, porting, everything is stock except Pipe, silencer, reeds, bolt-mod and timing. IMO, only, and correct me if I'm wrong, anyone, I have been wrong before, plenty, so don't take my opinion only, but if you are putting out more power than stock with mods like porting and head work, you would be richer than stock jetting. I think, to put out more power with a mod, it takes more fuel to run that mod. Otherwise, a stock motor should be close to stock jetting, with the main maybe two sizes one way or another, max. Clip position, would be stock or adjusted up or down one to tweek power delivery.
My theory is sketchy ,as there is always exceptions, PC actually recommends a clip adjustment to one leaner than stock. That confuses me. A worn cylinder and rings will often require richer jetting. I don't quite understand that. Its important to do one thing at a time, keep notes on settings, results and temperatures. Keep in mind a drastic temperature change (like 30 degrees) cooler will lean out the jetting and, if it warms up 30, it will start causing a rich condition. Any attemt to "fix" jetting that has no or poor results, go back to original setting before trying something else. Then make a note. Over time those notes will speed up the process for you.
Worn reeds, worn cylinders, smashed pipes, poor throttle cable operation, dirty air fiters, carboned up powervalves, old fuel, wrong spark plug, weak spark, worn carb, obstructed exhaust, or just about any uncontrolled variable will make it harder than without these hurdles.
Also, it is important to remember, mixture screws and needle adjustments, make a big impact. shifter cart guys will tweak mixture in the middle of a lap. Small adjustments can make a big difference. It may seem like you get the motor running right, but then notice it revs to the top of that gear too fast. Don't be afraid to go taller gearing when looking for more power. The 500 can pull taller gearing than a 250 comfortably. Check plug color when engine performance is in question.
By the way, the 02-03 Cr 250's are very fast bikes (case/reed motor). I read an article that said they were putting out like 8hp over previous years. And many hillclimbs, my kx250 runs a better time than the 500. I continue to tweek on it, but the 500 will never be twice as fast like expected. There are still all the factors like traction, gearing, chasis and fear probably, that seperates them.