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I have a 2004 cr250r that has no neutral, was riding it one day until it made a “clunk” noise. I then shut the bike off and haven’t tried to start it since, but ever since then every gear will work and shift smoothly except neutral and the counter shaft seal started leaking once this happened. There are metal shavings in the transmission fluid. Any idea what could of happened? Just had a top and bottom rebuild done with around 40 hours on it.

Hello, that sounds like you are going to have to go in for investigative surgery. Probably damaged shifting drum or a centering bearing. Metal in the oil is evidence of failure. Time to open it up.

Yea , I agree , it sounds like something gave way , what does the shifter do when you shift to 1st gear ?? , as it has to pass Neutral , does it do anything weird ?? , or just go right in and out of 1st into 2nd ?? .........(without the engine running and just rocking the rear wheel back/forth and shifting with your hand)

Most likely as Neil mentioned , the shift drum is chipped and/or the countershaft bearing possibly went and that is misaligning the shift fork , and that either damaged the drum , or is just misaligned ... but no matter what , the metal shavings is a indicator that you need to split the case and find what went wrong ......

Without the engine running it will shift into first and second just fine and does nothing weird, it just has no neutral. I guess ill just have to split the cases and do some investigative work.

I hate to do it, but that sounds like my best bet.

Yea , unfortunately that is the only way this is going to be fixed ...Keep us updated on the findings .... or if you have any questions .......