Skid,
The KDX will fit the bill just fine after some uncorking.
www.dirtrider.net/justkdx will give you the poop on this. IMO is it not optional, rather manditory that you do as described relative to the pipe, airbox, and jetting. That is unless you like riding a bike with the equivilent performance of having a potato stuffed in the exhaust ;).
Same for the fork springs. Not only are they light for your weight, they cause on unbalance of the bike front-to-back. Without this change the bike won't handle right under your gerth.
The good news is after about $300 and a few evenings you'll have just what you are looking for. The KDX is not unique in this regard. All US market "trail bikes", XRs included, need some minor work to get them up to their stock potential state of tune. Just comes with the territory of sound and exhaust emission standards (however this does not explain the KDX's stock rich jetting). While you have the front end apart to do the springs this is a great time to replace the stock bars. Something like a set of Renthal CR Hi bends will make the bike much more comfortable to stand on and won't turn into a pretzel the first time you take a good digger like the stockers will.
Sometimes the virtues of a true trail bike are overlooked. Glad to see you are taking this approach to dirt riding. I just did an XR250 in the past month, and man am I happy with this machine. Had a '99 KDX BTW so know this bike as well. Both are pretty different from my KTM 300EXC, but just as good of bikes in their own ways.