I just went through this on my 91 CR500R motor that I am putting into a 2004 CRF250 frame. There is a cert clip that is supposed to be in a grove just before the spring on the clutch side of the transmission. If someone tried to take off the shift lever and did not remove the bolt all the way (it is held back by a grove at the end of the shaft), they may have tried to force the lever off. This may have forced the cert clip out of the grove that locates it and will cause in and out end play. Remove the shift lever, then the two clutch covers and the clutch. Pull out the shifter shaft and look for the displacement of the cert clip. Also, check to make sure that the clutch side of the sifter shaft (if bent, it will not engage and shift properly) is not bent because it could have been bent a little if someone was pounding on the shifter lever to get it off.
See the attached image. Arrows show the cert clip and its proper location.