426 stuck in gear - won't shift

Just finished replacing water pump shaft and seals and put the engine back together and now I cannot shift the bike from whatever gear it is currently stuck in. It's been apart for several week so I can't recall whether or not I parked it in gear, or managed to shift into gear when the right side of the engine was torn apart or what I've done. The clutch works fine - I started it with the clutch disengaged and rode it up and down the driveway with no issue, less the inability to shift gears or find neutral. Shifter lever will move down fine, but seems to have a limited range of motion upward (stuck in first).

I didn't disassemble any clutch parts while the right case was off and the engine/transmission were performing flawlessly prior to teardown - less the water pump leaking coolant. I figure there's no way I'm not going to have to tear everything I just installed back apart, but was hoping someone has done this before that can tell me where to start.

Admittedly I haven't gotten a chance to look through the manual - I just came in from running it to check the oil after reassembly and have to knock off for the evening.

Does the shifter feel normal? How far from center will it move in either direction? Does it return all the way to center?

Did you accidentally goof up the shift drum and changer alignment? The claw thingy with the round thingy with pins on top :banana:

Unless there is a shaft that is not adequately supported when the right crankcase cover is removed that could have bound if moved when the cover was off, I don't believe I disturbed anything. It looks like all of the shifting linkage is far enough below the clutch that I don't have much of a chance of gaining access by removing the clutch cover only and pulling the clutch. Looks like it's all coming apart again.

The shifter will move ~1" down from the center or resting position and will not move upwards at all.

The reason I asked about the shifter is because the right crankcase cover keeps it pushed to the left and into place. It's easy to let it move far enough to the right with the RCC off for the centering spring to drop out of place.

Also, look at the point where the slot in the shift shaft lever arm engages the lever and roller in the end of the shift cam. Everything behind that is held in place by the guide plate.

You were exactly right - the shift lever slid over to the right when the crankcase cover was off and the slot in the shift lever arm disengaged from the roller on the shift cam. Wish I had been paying more attention during assembly the first time.

Two more questions came up as a result of having to pull the crankcase cover and clutch to get down to the shift lever arm:

1) What's the best way to hold the clutch boss while torquing the nut if you don't own the Yamaha clutch boss holding tool without damaging parts?

2) When installing the right crankcase cover, the service manual says to install the dowels, then the o-rings around the dowels, then the gasket, and then the crankcase cover. I followed that sequence and when I assembled the first time and the o-rings were shredded when I pulled it apart this time - enough that there was a small oil leak on the one down below the oil filter. Do they need to go on top of the gasket? I put in new Yamaha parts and torqued fasteners to 52 in-lbs.

1) If you have an impact wrench, throw a rage around it and hold it by hand. Otherwise, put the bike in 5th gear. The wheel will turn backward as you turn the main shaft forward, so stick a piece of 1x2 wood under the chain at the rear sprocket, and/or a plastic hammer handle through the rear spokes under the swing arm.

2) Look at the holes where the dowels go into the case. If it has a recess cut into it, that's where the O-rings go. Yamaha expects you to put the dowels, rings, and gasket on the case cover, and put all of it on at once. I do it the other way. It doesn't matter, as long as the O-rings sit in the pockets cut for them.

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