Dan,
The hard hit on power delivery is probably a manefestation of the pipe more than anything. Most motocrossers use a pipe that does not work as well for off road, so first thing to do is find out what pipe you have.
Next, you need to make sure your power vavle is working properly, so pop that cylinder off and clean the power valve. This may be your only problem.
To continue, DO NOT add a flywheet weight to a 250, as I don't think you will like the result. The reason it works for some (old guys, right Paul) on a 500 is because the 500 has the power to run the weight. While I do run one on my son's KX125 in some situations, it is meant for to solve the complete lack of bottom end on a 125 for deep sand corners, a problem that is not present on a 250.
Run a NGK BR8EVX plug in the 250. More expensive, but you will not be disappointed.
You don't need a reed spacer on a 250, so save the money.
In a nut shell, the 1999 KX250 works well without spending a lot of money. Focus on suspension, getting the power valve cleaned up, running the right pipe, and installing a stabalizer and you will be happy as a clam. (hand guards, skid plate, etc. are a given)
Good Luck
Rick