If the power valve is stuck open, it most certainly will kill the bottom end power.
Check the powervalve operation as Darringer instructed. All you have to do is remove the inspection cover (one 17 mm head) on the left side of the cylinder, start the bike and rev it up. Have you done that yet?
If the end of the shaft does not rotate from the closed position to the open position as revs rise, you did not properly line up the linkage to the powervalve when you put the cylinder back on. This is a very easy mistake to make on your generation CR250.
If the powervalve is stuck open you will need to lift the cylinder from the crankcase and try again to line up the linkage properly.