Transmission Problems

Well, I was riding at the track yesterday when all of a sudden I had no 1st gear. All the way down was neutral!! The shifter felt as if it was trying to shift, it would go down but would not engage 1st gear. I let the bike cool off and tried it again. Everything was OK until I couldn't shift out of 2nd, no 3rd, no 1st or neutral. After going over a few bumps it started shifting again but it was very clunky and sometimes felt as if it didn't want to go. It seemed like going over bumps and shaking the bike around would make it start to or quit shifting. There were no horrible sounds coming from the transmission, nothing out of the ordinary KDX noise. It finally stuck in 1st and the day was over. I let it sit at the truck while I rode my buddies YZ250 (holy crap!, FAST) and when we went to load it up it still would not go into neutral easily. It took a few minutes and rocking back and forth in gear and it finally went. Sometimes when it would stick in 3rd I could press down on the shifter and it wouldn't budge, sometimes it would go all the way down but not shift, occasionally it would shift. When I got home I put it up on the stand and in neutral I spun the back tire. There is something knocking in the transmission. Everytime the front sprocket makes a revolution there's a KLUNK, this is much worse if I spin the tire backwards. I know it's time to rebuilb and replace broken parts in the bottom end :( Does anyone have any idea what has happened to me gearbox or have any tips or experiance with this sort of failure. I will be doing the repairs myself exept for splitting the cases, yes I have a manual and all the right tools but have never been in a gearbox. Thanks for any help you can give!!

KDXTreme
1998 KDX 200
Airbox mod, 155/48, FMF Gnarly Woods, Broken Gearbox, ETC...

Well, unfortunatley, that's not it :( I took the engine apart last night and got the entire right side off.. Clutch and all, I found alot of small metal particles in the bottom of the case.. not the normal micro particles from clutch wear but rather large ones >:( I also found that part of my right case had been bent and was almost broken off inside the engine. It looks like part of an oil channeling wall. The break is directly above where the idle gear is at about a 1:30 position on the idle gear. The piece was bent down and was almost touching the idle gear, I finished the breaking-off after I got the idle gear off, I should be able to hone that down to a smooth edge and it should be OK unless someone knows that this will not work and that the oil must be channeled specifically through this area. It looks to me like the only way a break like this could have occured is that something lagre and metal must have become lodged in there somehow and been foced in a way which bent the case internally. There has GOT to be something foating around over in the transmission so now I have to split the cases, I could find no damage anywhere in any of the gearing that I have gotten to so far.. The shift return spring and shift mechanism were undamaged and would actually shift with no problems when I tried it with the cover off.. Basically I just have to keep digging. Anybody have any ideas what I may find?? Also, I plan on taking the cases to my local shop to get split and then doing all the internal repair work my self, I am a good mechanic. I have never been in a bottom end, how much of a pain is it to get them back together right? Is there anything in specific I should look out for? Are there any specialty tools I REALLY need.. Like the crankshaft jig?? Or should I replace all the broken parts, get it all ready to go back together, then take it to my local Kawisaki shop and have them do the re-assembly with all the right jigs? Thanks alot for any help!!

Yep, the pin is in place. The KIPS valves were working fine, I can tell when they don't as my powerband shifts drastically depending on whether they're stuck open or closed. I do alot of shifting without using the clutch, perhaps I've broken a shift arm but I don't know for sure.