I am not really understanding what is going on...
.. OK...With ALL the clutch components and the drive chain removed - can you (in each gear) SPIN the main transmission shaft ALOT( 20+ turns) in the correct (drive) direction?..I think its counterclockwise.
It is important to remove the drive chain and all clutch components to do this check. You are checking for a SINGLE CRACKED GEAR TOOTH .. the crack will be at the base of a tooth.
Do this check exactly as described.. you are checking the functionality of the transmission alone. - no clutch-no drive chain. If you do have a cracked tooth, the transmission will only rotate about 340 degrees in either direction.
If it was the clutch giving the problem, it would happen in ALL gears...
After the check.. repost and we'll go from there.
SOURCE: '95 Yamaha YZ 125 clutch - stays in gear when clutch is pulled in
the plates will stick to each other because of oil
check the clutch lever at the motor and make sure it is moving the arm that pushes the pressure plate and make sure it is moving
SOURCE: Clutch Adjustment Issues / 78 Yamaha XS 650
Disconnect the clutch cable at the case then see if the there is any resistance in the clutch lever in-out movement. When the tank was remounted the cable may have gotten pinched or moved out of proper routing. If I understand correctly, prior to the frame painting the clutch was okay, but after the paint it was not, and the left and right side cases and clutch were not touched. Obviously you used the wrong brand of paint. The clutch would have been fine if you had used Krylon brand paint. Post a comment and let me know what you find.
SOURCE: Clutch push rod will not depress to engage
go to this http://www.cmsnl.com/yamaha-rt1-19701971_model8356/partslist/A-09.html and then click on "view big image", this will give you a diagram of the clutch etc,, the adjustment (No. 26) may need looking at, or (No.11,12,) have broken.Basically you turn 26 in (clockwise) untill you feel light resistance then back off 1/2 turn (been years since i worked on one of these!) this should give you freeplay, have you just got the bike?, and do you think it has been stripped lately(ie the clutch). PS I am not affiliated with the web site i offered above, just a handy reference for you maybe? cheers
SOURCE: Yamaha YZ125 Clutch not disengaging
I would be more concerned with the stuck gear than the clutch, but we will start with the clutch.
The push cam may be bent or deformed and the push shaft may be bent. Assuming the ball bearing is in place, the cam and rod are all that can really go wrong. The rod slides out of the left center case. You will need to loosen the springs to get the left side cover back in place. Roll the rod on a flat surface to see if it is bent. I fear a bent shift fork is causing the gearbox to be stuck in third. Fix the clutch and then post a comment to get back to me.
SOURCE: 2005 TTR 125 will not shift into first gear
This is one of those issues that is really tricky to diagnose over the net but would likely take a few minutes to diagnose in person.
When it does drop into gear, does it jump or stall? Will it idle in gear, stopped with the clutch pulled in?
My initial thought is that the clutch is not being fully released (the plates are still in firm contact with eachother).
More than likely, the resolution is a fairly simple adjustment.
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