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Discussion Starter · #1 ·
OK i tried looking for any threads about this but can't find any. I'm rebuilding my99r6 engine along with fixing famous 2nd gear problem. I have several questions..

1: What should/needs to be replaced?
2: what are things to look for in rebuliding an engine/trans?
3: what would be good upgrades to do in engine/trans ?
4: best place to buy the parts at?


any other info/comments would be greatly appriciated.
 

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2nd gear link

also it would help to know what your purpose of rebuilding the engine is for. do you want to prep it for supersport class or just to be rideable again?

i think the other common things are jetting it and maybe an ignition advancer. other than that i think the engine is solid as is.
 

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Discussion Starter · #5 ·
i have a 2nd stage jet kit, micron full exhaust and power comander.....the famous 2nd gear is fukd, shift really hard into 2nd and then it keeps slippin if i hit the throttle to hard... so i wanted to just tear it apart and make it new... good idea or not??
 

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Discussion Starter · #7 ·
whats your point? You asked about how to fix the trans and I told you a common fix. I dont see what you are trying to say
I'm tring to understand what you have mentioned about puttin in a 2nd gen trans, is that just a simple quick fix? my intentions are to rebuild it as if it a new one. now back to my first post...........
 

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i have a 2nd stage jet kit, micron full exhaust and power comander.....

Explain to me again how you have power commander? Those are only for Fuel injected bikes. So you have both a jet kit and power commander. If you really believe you do, then you got jipped!
A good fix for your tranny issue is to swap in an ENTIRE tranny from an 03-05 R6. Or you can replace the gears that need replacing but you still have the risk of it happening again.
 

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I "rebuilt" a 99r6 motor, because of the 2nd gear problem. There should be plenty of info on this site about it if you look hard enough, as I used this site to do mine.

I can't remember where I got my parts, but it was just some online Yamaha OEM dealer where I found the cheapest parts, just look around a little.

You won't know what you need to replace until you get it apart. I spent roughly $600 but ended up replacing shift drum and timing chain which I wasn't expecting. I had the "engagement dogs" of the gears "back cut" instead of replacing them and would highly reccommend it. It wasn't much more than getting new gears. I think it was $250, but it was money well spent as no problems 15000 miles later.

As for the crank, head and pistons/rings-I left them alone, besides basic clean up of head (visable carbon deposits). In retrospect I might of should of replaced the rings, as the bike smokes some (not much). Do a valve adjustment why you are at it, with the motor out it takes no time at all.


It was a fairly straight forward job. I got most info off this board and you must have a yamaha factory manual. You will need a good torque wrench and basic tools plus the obligatory odd tool/socket here and there.

If you have never worked on motors at all ever, you still should be able to do it yourself if you are mechanically inclined, semi-organized and patient. But if this is the case you better know someone who can come over and help you when you get stuck.

As for how long it will take you, it depends on having the parts ready when you need them and so on and so forth. I have heard people say they did it in an easy weekend but it took me much longer than that.
If you are just going to work on it in your spare time ordering parts as you go, adding in waiting on machine work, it easily goes into a month or two.
 

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power commander will be a box under your seat most likely.

i will bet 1000 dollars you DONT have one since its carbed. if you do its just adding extra weight take it out and sell it on ebay.

jet kit will be a little more extensive and to be honest i dont know how to check either.

if someone could provide info for us...
 

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2 gear/ transmission swap

Hello,
My 2001 R6's transmission seems to work great, except half the time shifting into 2nd, sometimes it grinds terribly, but once its in gear, it never pops out. Would swaping the transmission for a 03-05 transmission fix this as well? Is it worth the price? Where can I find one of these, and how much work would it be to install? I just bought the bike 2 days ago so I don't know much about it yet.
Thanks,
 
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