Yes, this kit will include the Valves. If you need to replace the shaft or any of the other parts associated with the power valves you can find them in our O.E.M. section for your 2000 YZ125 here:
The Athena Factory Cylinder kits do require you to use their piston. If you purchase the cylinder kit, it is complete with cylinder, head, gaskets, wrist pin bearing and piston kit. Keep in mind since there was no model listed, this is not available for every make and model.