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when my bike is running I can't shift into neutral from first. When I accelerate through first gear and go to shift into second its fine and when I turn the bike off and rock it it will shift but while running there's no way its moving from first while stopped. Its a hydralic clutch and I have flushed the fluid and tried bleeding it many times but this doesn't seem to be the problem. I can't see any leaking anywhere either. are there any adjustments I can make?
 

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This is a Yamaha problem, similar to ones I heard of on the FJ1200 board when I had one of them. It may be simple like oil or a dragging clutch as pointed out, but it also may be bent or worn shift forks in the tranny $$$$ especially if it has been abused (which would show up first around the 1-2 upshift).
 

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If the clutch is dragging then it can make it very hard to try to catch neutral. Is the bike trying to creep ahead on you when you have the clutch in and in first? If so then your clutch is not disengaging all the way.

Dragging like this could be due to a couple of things. First is that your clutch hydraulics may not be working correctly so you're not getting the full throw. But usually if it's not leaking from one end or the other then that should be fine. If your fluid level is staying steady then it's most likely fine.

Next is the actuator rod and throwout bearing. These are the parts that connect the slave cylinder travel to the clutch pressure disc. If the bearing is hooped it may be wearing down the rod since the rod isn't supposed to have a spinning part running on it's end. Or it may be as simple as the bearing blew and let the rod move in further. Often the clutch slave is on the other side of the bike from the clutch and the actuator rod pushes on the pressure disc from the back side through the shaft which is hollow. If you remove the slave you should be able to see the stub of the rod. Measure it up and see if it's sticking out the right amount.

Another cause of high clutch drag is one or more plates being badly warped. When that happens they spring out like spring steel potatoe chips and maintain a lot of clutch drag even when the pressure disc lifts the correct amount. There are specs for how much warping is permissable. It's so little that you need a feeler guage and a known flat surface to test it. A square foot of 1/2 inch window glass is a nice testing surface.

Now if it's NOT a draggy clutch then it may well be a bent shifter fork or worn selector pin or some other cause inside the transmission. But I suspect not since you're not having any troubles with shifting while moving. Perhaps try finding neutral from second while you're rolling down to a stop. Is it easy to find when you do that?

Assuming it used to be a nice slick shifter then I'd concentrate on the clutch related items first. Check the rod and end bearing and check the clutch pack plates for warping.
 

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Late as this may be, I'm going to throw in my experience on a cable clutch. I was having the same issue on my 2015 CBR1000RR. I was so accustomed to having hydraulic clutches on my bikes that I never thought much about it let alone that I could simply adjust the cable ( at both ends ). The nickel finally dropped down in Weaverville, CA. I adjusted it and all was good. On the way home way out in the middle of Nowwhere, Washington, I arrived at a stop sign and I could barely get the bike to come to a stop while in gear. I looked down at the adjuster and could see that the cable was down to just 4 or 5 strands. So, not only was the cable about to experience a sudden death but there were so few strands left that it took very little time for those to stretch enough to make getting in and out of neutral while stopped almost impossible.

The rest of the story : I got to Moses Lake an hour later and spent the night. Soap Lake is right on I-90 so I slabbed it all the way to the border and shifted without the clutch the whole way. Just one gas stop so I had have a Plan B in my head in case the cable snapped the last strands. Fortunately, I had a spare cable at home which my brother retrieved and had waiting at the Chevron just north of the truck crossing.
 
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