There are some simple things you can do to any bike with dual disc brakes.
First off install new slide pins for the pads. The stock ones get grooves cut in them and the pads will not slide freely as required. Also install new DOT 4 fluid after flushing both the front and rear systems.
Second, install some new pads. Get some upgraded compounds like the Braking C44 units. Semi/Ceramics. they work really well for me! Only bad thing is that when hot, then can make a bit of noise. But the improved braking is worth that to me. the rear is the worst.
Third install new brake lines. The SS units will resist expansion more than rubber to give you a better, firmer feel.
Lastly, adjust the front brake lever and inpsect the rear pedal. If you have to much slack before you start moving the MC piston, you are going to have to really grab to start braking. not fun! The front is really easy. For the rear inspect the pivot point and the hole for where the bolt mounts to the MC plunger arm. That hole will elongate and thus give you a lot of slack in the pedal without any movement of the MC! The KDX bikes usually have steel rear brake pedals, so they are easy to weld and redrill the hole. Just did that to mine and made a huge difference!
Other than that, replace any parts as needed like the levers and seals. Be sure the disc are in good working order and do not need replaced. If you need new ones, check with
http://www.rockymountainmc.com for some Titax brand units. they are $50 a wheel brand new.
Hope that helps you