When you put the cylinder back on, it is possible the little fork that operates the powervalve was not positioned properly, and your power valve is either not opening or stuck open.
This is an easy mistake to make on the '92 - '01 CR250 motors. You need to really make sure that the little fork and shaft at the bottom right front of the cyliner lines up exactly right. If you are not aligned properly, you will have to remove the cylinder again to get it right.
There is a powervalve inspection cap on one side of the cylinder (left side, I think). You can remove that cap, and start the motor. Rev it in neuetral. When the revs build, the powervalve shaft should turn 90 degrees from closed to open.
Also, the only time my old '99 CR250 had trouble starting, it is because the reeds were bad. Even a slight warp or crack can make it very difficult to cold start.
But sounds like you have a new problem.