In general terms there are probably two key areas to look at, the RC Valve circuit and the regulator.

Disconnect the RC Valve motor and put a voltmeter across the battery, it should show about 12-12.5 volts. Start the bike, voltage should now be somewhere between 13.0-14.5volts. Any more and the regulator might be cactus, stop engine and replace. If the voltage is OK, slowly increase rpm, voltage should still be between 13.0-14.5 volts. More the regulator is stuffed, stop bike and replace. Less and something is drawing excess power. So you would need to go through a series of elimination by disconnecting parts of the harness.

If voltage was OK then go through the RC Valve adjusting procedure here -> http://www.nsr-world.com/tuning/250-tuning/engine/ . Making sure to check that the valves and cables move freely through the full range of motion, and have enough slack. Poorly adjusted or sticking valves or cables will make the RC motor draw extra current, and as the power circuit goes through the PGM this burns it out. When you conect and disconnect the TPS the motor should rotate and stop. If it all appears OK, run up the bike again and check the voltage through the rev range with the RC Valve motor connected. If the voltage drops off the RC valve motor itself could be stuffed.