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Just registered to this list to see if I can get some information. I purchased a used 2001 K12LT in 2013 with 84K miles. Over this past winter had the dealer check it out for level 1 service at 94K miles and they found a leaking rear transmission seal. As part of the service I had them replace it and have the drive shaft and splines lubed. After getting it back I noticed that there was a slight knocking noise that I had not noticed before but did not think much of it. Have put 3K on since spring but after a 1K ride in June I started to notice another noise when running in second gear(and only 2nd gear). Best description I can give is it made me think I had a front tire rubbing intermittently on the fender. It has gradually become louder and louder, now sounds like I have a hydrostatic transmission from a tractor on the bike. Most recently it is difficult to shift, now and then makes a clunking noise when letting out the clutch and sometimes stays in between gears. After consulting with dealer they say it may be the transmission but I am thinking it may be other things like the slave cylinder. Anyone have some experience with this? I did check the linkage and bolts that hold it in place and everything was good.
 

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shifting could be the linkage ball joints need to be removed and serviced, it could be the slave cyl bearing, best guess is transmission failure possibly input shaft brg, you should stop riding and fix the issue, unfortunately you were only an hour away from removing the tranny when they did the rear seal, when you pull the tranny and I think you should, pull it down and inspect replace the front bearing replace all the seals remove the clutch and replace rear main seal and O ring. Oh and this isn't going to be cheap if you are paying a dealer.

edit: there is a 2003 being parted out on the site with low miles you might check it out,
 
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I have not heard it myself ( yet) but the noise you are describing does sound like what others who have had the transmission input shaft bearing go out describe. It is a sealed bearing so it has nothing to do with transmission oil type or how often it was changed. I agree with Axle, it is something you should stop and fix or have fixed.
 

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Time for some evaluation as to the bikes value to you. Yes, you need a transmission overhaul. With it out you need to replace the 19x4 Oring in question. Then you will have another 100000 miles of riding.
Here is a thread on the Oring and how to get all this stuff out of the bike. If your handy you can do it over the winter (heat in the garage I hope!). A bearing replacement and all the tranny seals except your good one should be all you need there if you don't ride it any longer.
 
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