I recently bought a 2005 crf250x and decided to change the oil first ride in after I noticed a "chinking" noise at low Rpms. When I went to replace the gearcase oil there was nothing in it. I'm assuming the guy before ran it like this for awhile. I filled it up, took it for another ride and now the clutch doesn't engage. I know the clutch is most likely burnt out but could the damage extend to vital engine components and how do I check?? Any help would be appreciated.

well start by pulling off the right side case. To do this you need to drain the coolant also. Any bearings that are in there are now junk I'm assuming. clutch plates are most likely junk like you mention.

So start by taking off the right side cover and see whats damaged.

Ok I will do that today. To replace the bearings am I going to have to split the case? If I do then I'm just going to get the bottom end rebuilt

I would replace clutch plates, fill with oil and see how it rides... then go from there.