2002 kx250 poewrvalve question

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Hello, I'm new here just found this site. I recently bought a 2002 kx250 and I'm putting a new top end on it and cleaning the powervalve. I went to re-assemble the powervalve according to the manual, and realized that with the manual instructions, the powervalve didn't seem to operate correctly. I can get it to look correct (valve alignment), but not using the manual suggested alignment of the rack and gears. Has anyone else experienced anything like this? I have a thread about with pics on another bike site http://www.thumpertalk.com/forum/showthread.php?t=576268, not trying to promote another site but it's a long thread with pics so it would take a while to transfer everything here. I know I should have paid closer attention when I took it apart, but I had the service manual so I thought I was covered. Thanks for any help or information.

[Danger4u2]

Here's info on the KX500 it might help or give you some ideas.
http://www.hallbergs.net/kx500/#41

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Thanks for the info, I finally got it figured out. I thought that when the slide valve reached the end of the travel, that the side drum valves also had to stop moving, but they can actually continue to rotate further due to the spring on the silde valve. I hadn't factored the extra spring travel, and thought something was way off. Next time I'll know! Thanks again for the help!