2002 suzuki rm 125 shift drum placement, shifting problems,

I have had a bunch of problems with my 2002 rm 125. I have replaced the clutch, oils, etc. What had happened is that the bolt that holds the shift fork in place had broke away from the crankcase. I took the motor old and replaced this crankcase have with a good used one. I rebuilt the bike and put it back together, cleaned everything and even repainted it all lol it looks new. Anyways bike starts first kick like it should, shifts into first gear excellent without stalling, jumping etc like it should, but I only have first gear and neutral. I know I should have checked that the bike shifted properly before I put it all back together. Now what I think has happened is that the shift drum had somehow got moved during assembly, now I didnt take the drum or anything out of the cases I didnt have to. Any info, ideas solultions would be great, this has been taking way too long to put together lol but no rushing hear. Also if anyone can tell me where I can a diagram showing the proper lining up of the drum etc before assembly to see if it is right before I put it all back together. The shift fork, etc all look good. Could the rould part with all the gear grooves that goes behind the clutch basket and against the case have be the problem? Any ideas or suggestions would be great thanks again