I had a 99,00,02,03 YZ250. They ran great and I never had any issues at all.
You need to rule some things out:
Do a compression check, look for 180+ psi on a stock YZ250. Make sure your using fresh premix, replace the plug, check for vacuum leaks around the intake, re check your power valve linkage, clean your air filter. If all of this checks out fine you will need to test the coil and ignition systems. A shop manual will give details for the trouble shooting process.
Good luck...