What bolt on mods have you done already? The Kdx doesn't have the best suspension in the world, and without suspension mods you'll really struggle to use all of the bikes power with just bolt ons such as reeds, pipe, air box, jetting etc. having said that, I weigh 63kg so power isn't so much an issue for me as it is for others.
I'm yet to come across a 250f that is faster than my bike too. I suspect the 6 speed gearbox has much to do with that though.
I'm assuming you're having the cylinder bored and not plated? I wouldn't like to play with porting on a freshly plated cylinder. You might consider having the head machined to improve squish. Apparently the head work really makes a difference