Just give a little background on where all my test/tuning has been is with converting MX bikes to compete in east coast enduros with for the past 14 or so years. I've converted/competed on '00 CR250, several '03 & '04 KX250s & a '07 KX250 (and now back on a franken-biked '03/04), besides riding tons of different enduro bikes, KDX's, etc over the years working in the motorcycle industry.
There's a couple of ways you can go about trying KDX'ify your '03 KX. The resounding trait of a KDX motor in stockish trim is seamless power and loads of grunt (more then any 200 has a right to). Best way to acheive that on a '03 250 is to fill in the gaps in the low-mid power delivery, lower the gearing and slap a heavy flywheel weight on it (or E-line lighting coil) to get that idle to nothing, tractable pull from the bottom of a hill kind-of-power. Easiest way to acheive that is get an '04 engine and slap it in a '03 chassis (seriously, '03s have great forks for trail nasties and a linkage to match, but the linkage set-up does give it up to the '04 when the rocks turn to sand whoops). The '04 engine was literally one of the best MX convert engines of all time that I've ridden/raced. Smooth, tractable and a seamless, meaty power delivery from idle on up. The next best thing, to do with a '03 engine for a KDXish power delivery without porting is as follows:
-Pre-Load Powervalve Spring w/ Spacer/ '04 PV spring
-FMF Gnarly Pipe (a must for grunt, I've run 5 different pipes on the '03, ths is best by far)
-Either a V-Force (2 or 3, but get used to replacing reeds) or Boyeson Pro-Series Reeds (must be for a '03) on Stk Cage
-The Turbine Core silencer is fine in length, just keep the packing fresh
-Flywheel weight, 11 ounce is a good choice (I've used none, 9oz, 11oz, 13oz & a E-line Lighting Coil, the coil making the most drastic difference.) Yes, response will be slower, but that's what you're looking for when in need of enduro bike/KDX power/tractability (which the '03 engine lacks, thanks to the PV slamming open prior to the bike being ready to run on the pipe).
-Final Gearing, I've used 13/51 & 13/52, 13/52 is perfect in my book, I like to have the power on tap and we don't have much for high-speed stuff.
I've tried plenty of other mods (different black box, Power Now, etc), but what I listed here I felt were the best spent money besides keeping the engine fresh.