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Discussion Starter #1 (Edited)
Below is a small summary of my repair on my 1999 R6 which has second gear pop out. The bike suffers from popping out of gear around 10K rpms. This is attributed to worn dog bones on the 2nd and 6th gear respectively. I did not document every step, but the pictures and parts list should help others with the project. By the way, I do not take any responsibilty if you damage your bike or hurt yourself or others, I am only posting this to show my experience.

The project took me two days to complete with 4 trips to the parts store. Even without the additional trips to the store it is still a good 2 day job.

Parts list:
What I used, from ronayers.com:
93102-35423-00
90215-21022-00
5EB-15451-00-00
5EB-13414-00-00
5EB-15456-00-00
5EB-15461-00-00
5EB-17221-00-00
5EB-17261-00-00
90506-13535-00
93440-28062-00 - Three of these are reqiured...

Total in parts was about $130.

There are other parts that have also been recommended to replace, such as the shift forks and cam assembly. I am cheap and took a chance that all of this is still in working condition, it also knocked $200 of the cost of the project...Go here for the additional parts list:
http://www.r6messagenet.com/forums/r6_warranty_and_premature_failure/1512-99-02_r6_only_2nd_gear_slippage_problems_-_warranty_issues-49.html





Basic tools like a ratchet and allen wrenches are required, as well as snap ring pliers and a torque wrench. Tool girl and tools needed:




Remove all the platics:




Remove Gas tank, remove seat, disconnect battery:




Unbolt Header and remove complete exhaust, make sure not to loose the gasket inserts for the header:




I only detached the chain from the front sproket, but you are better off removing the front sprocket since you will want to replace the oil seal behind the sproket during installation:




Disconnet all the wire harness sensors on either side of the engine. They are basically color coded so it will be easy to reconnect them. Make sure you undo the zip ties so that all the sensors connected to the engine will not get stuck when you lower the motor.




Drain and remove the radiator, make sure to disconnect the fan and plug and temp sensor, as well as all the hoses. The radiator bolt on the clutch/left hand side of the bike will disconnect it from the support:




Remove the air filter/intake and stuff some paper towels in the Carbs as a precaution from falling objects. Double check that all the electrical plugs are disconnected and placed out of the way. You also need to disconnect the Clutch Cable, Choke, and Throttle Cable. The clutch cable is simple, as well as the choke, but the throttle cables are hard to get at. I found it easiest to just unbolt the bracket for the throttle cables. I used a simple car jack and piece of wood to lower and support the engine. It is much easier of you have two people for this part, the tool girl was required to help role the jack in my case. It helps to get the bike a few inches higher, so if you have a stand for the front, use it:




Here is how it all looks once the engine is out, this is about the 40% marker. These bikes really are just an engine and tires:




Now for the fun stuff, you will need to remove just about every cover on the bike, start with the oil pan:




I would highly recommend some sort of professional book at this point, beyond this you will need to know torque specifications for anything else that is removed. Remove the stator/alternator/generator (what ever it is called), pay close attention not to disturb the gears on the top. They want to fall appart when you remove the cover because the gear shaft seats in the cover, also the cover has a bunch of windings and the magenant will try to pull the cover back onto the engine:




Remove the clutch cover and the timing chain cover, when removing the timing chain cover there is a small rod that wants to pull out with the cover, try to keep it attached to the engine, sorry I forgot to get a pic just keep it in mind:




Now it is time to separate the men from the boys. The next step will be to remove the lower engine cover. Remove the metal radiator hose from the front of the engine, you should be able to see that it will get in the way once you start to separate the lower engine half. Double check to make sure that all the covers and parts on the engine will break away freely once the lower cover is removed. Remove the oil strainer thingy, the oil pickup line, the C-shaped oil hose, oil pump strocket cover, and the oil pump. Most of these are easy, for the oil pump I had to stick an allen wrench into the bolt hole and twist the dowel out so that I could detach the chain from the sprocket. Sorry I was too dirty to get pictures of this...but is self explainitory.

I used a guide to determine the order and where the 27 attachment bolts are for the lower case. Unbolt and carfully remove the case. At this point the main tranny shaft will be free, so be extremly careful not to let it drop (depends on the orientation of the engine if it will drop):




Here is a shot of the case once it is removed:



Here is a shot of the bolts laid out by number. If you look carefully you will see that some are missing, I left 4 bolts on the case to get out of removing additional parts. Specifically the oil filter thread, the large radiator hose on the right side of the engine, and some other cylinder that coolant goes into. I just loosened the bolts and then let them set since they were basically locked with the lower engine casting:




Carefully grab the gear stack, take note that the end oposite the front sprocket does not have anything to hold the gears on the shart. Be carefull that the gears to not fall off the shaft. Next I simply pulled the gears off the shaft, one by one, and placed them onto a clean surface exactly the way they were removed:




Here is another shot with additional gears removed, you also need some snap ring pliers to remove and install the gear retainer clips:




Below are some comparison shots of the new and old gears, the pics do not really do it justice:












Here is a shot of it all completed, I also used engine assembly grease on the bearings. Engine oil could also be used and should be applied at least between the new gears and the respective bearings:




Reinstall paying close attention to the orientation of the gear shaft. Cafefully place the shift forks back onto the landings, ensure the lock ring seats straight, and make sure the pin on the large bearing is rotated so it seats in the correct slot:




Torque all the retaining bolts properly and follow these directions and a good manual for the reverse order of installation items... Good Luck:

 

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..I should be working..
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Wow that is one detailed wright up good job on it!!
 

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I just wanted to thank you for the incredibly helpful writeup. My 2nd just started going out on my '02. I have no experience at this kind of thing, but I may have to try it since I am too poor to pay a pro. Thanks again.
 

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Discussion Starter #11
Keep in mind that you will need to be workin on the bottom of the engine. I used an engine hoist to hold the motor at the appropriate angle. If you just turn the engine upside down you will need to protect the carbs somehow. It is also a good idea to check the valves after flipping the engine to make sure all the components are still in the correct places...
 

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He be beastin
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Hopefully I will never need that writeup but it would probably be a fun project.
 

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great write up!............ my 2nd gear also just started going..... man I would love to just buy these parts and pay someone to do this for me, seeing as my young as shit and i know for a fact that i would fuck something up.
 

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Discussion Starter #16
Yamaha fixed the issue for the 03 bikes. The 03's have 5 dog bones on the gears, I had asked on the forum if it would be possible to use the 03 2nd gear in a 1999-02 bike. The answer was no, but it would be interesting to see what would happen if someone tried it...

It seems like it would work, if the dog bones was the only change...
 

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I heard you could do it, but you have to change the entire transmission... But, this is just what I heard and I don't know of anyone in pictcular that did it.
 

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So what exactly happens to the 2nd gear? is it those 3 stubs with the wear on them? the actual teeth on the gear looks fine. Also, are the new parts from ron ayers updated and stronger so the 2nd gear problem wont happen again?
 

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Discussion Starter #19
You can see wear on the 2 gears that I removed, it rounds out the dog bones as well as the slot on the other gears mating location. The 3 stubs are the dog bones( I think). They mate to the side of the other gear. The actual gear teeth do not have a problem, these are always engaged, the moving portion is the side of the gear. The new parts are just new, I expect that with correct rev match shifting that the 2nd gear should last a while (20K mi, would be fine with me). It is only a $130 fix, I think there is a way to perminantly fix the problem though you need to either completely rebuild the gear box with 03+ parts, or buy an 03+ gear box setup... Much more expensive...
 
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