How to: Teardown 98-01 R1 Transmission to fix 1st/2nd gear Issue. : Yamaha R1 Forum
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Old 10-06-2011, 11:10 PM   #1
99zPheonix1001
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How to: Teardown 98-01 R1 Transmission to fix 1st/2nd gear Issue.

2001 Yamaha R1
1st, 2nd gear replacement and engine tear-down.
I had a problem with my 1st gear and 2nd gear popping out and into Neutral and this is what I did when I decided to tare it all down. Ill keep it as simple and possible. And include as many pictures as I can.

tools are going to be pretty basic here since i didn't want to fork out the $ for any specialty tools, main thinks your going to need is a decent set of socket set and a Allen key set.

plenty of thread-lock (for when your ready for reassembly)

and all the gaskets for all the covers and engine crank (for when your ready for reassembly)

1. First thing get your bike on both front and rear lifts and remove all the body plastics.
2. Remove the front seat, gas tank and air-box.
3. Carefully find all the connecting wires that are connected to the engine from the body of the bike. Should be about 10-13 connectors. As well as all the coolant hoses and remove the radiator as well as drain the oil before getting ready to drop the engine.
4. When disconnecting the throttle cables I found it easier to just disconnect it from the handle bars.
5. Once you have that down and there is nothing else connected to the engine from the bike you gotta get it ready to drop the entire engine.



6. Now to remove the engine I used a normal car Jack and a 2x4 piece of wood. You should have a friend with you for the lowering part of the engine since it will get out of balance.
7. Once you get all the mounting bolts out you should feel the engine move around a bit.. once you start lowering the engine try and keep it stable so it doesn’t fall over.. now once I had it out from under the bike I was able to pick it up and set it on the ground



Once you get the engine out you will need to flip it upside down.. now to keep from damaging the carbs I went ahead and took them off completely.
Removing the engine isn’t really a hard task but it takes a little bit of time.. sorry I didnt include full detailed description how to do it but its really not that hard and shouldn’t take more then about an hour or two if that.
I used a engine hoist with a chain attached to it and a used tire I had in the backhard.. you may have to find your own way to get it upside down and solidly placed to where it wont fall over.
If you don’t have an engine hoist then a couple guys shouldn’t have a problem flipping it over.. I wanna say it weighs about 180-220lbs if that.

so you already got the engine out and your ready to flip it over.. before you do so go ahead and remove the clutch cover, the stator cover and the timing chain cover off the engine before flipping it over unless you can take them off with it upside down.. i found it easier to go ahead and pull it off while it was right side up.






ok so you got the engine out and got it flipped upside down and ensured that its stable and wont fall over.. now its time to start the real project and start getting everything out. you will 1st need to get your Allen key set out to start unbolting the lower oil pan cover off. there will be 14 #5 bolts around the entire edge of the pan and one 8mm bolt in the center that will have to be removed. once you have all of those out you should be able to pull the oil pan cover off and start getting a little dirty with the internals.





now in my case when i took the 1st cover off i was surprised by chunks of metal laying in it.. which i later found out was one of the springs from the clutch basket that had broken off and then shredded to pieces. but no big deal lets keep going. once the main cover is off you will need to start unbolting the oil pump out of the way but before you do that you will need to remove the 2 coolant pipes that are attached to it.. should be just a couple of allen bolts and a little elbow grease and they will come out. once you have removed from hoses/pipes unbolt the oil pump, now there will be a chain thats also attached to the oil pump you will have to remove it before you can pull the pump off, once the pump is unbolted work the chain out slowly and pull off the pump it self, and it should look something like this.





once the oil pump,strainer and chain is disconnected you can go head and start unbolting the lower case from the engine. there are i believe 28 bolts in total.. most of them are 10mm the rest are 12mm you will also have a couple of bolts inside the engine you will have to take off 6 are right by the crank and the rest are just before it. now the manual says to do it 1/4 turn at a time but i went ahead and just took them all off without any pattern.. once you have all the bolts out you will also have to remove the stator/flywheel cover i didnt have a stator removal tool so i went to a local hardware parts store and picked up a 16x1.5 3" long bolt and used a impact gun and the cover came right off. once the stator is off you will have to go back to the other side of the engine and remove a bracket that holds that chain to the oil pump so that its no longer hung up on the bottom of the casing.. once that chain is off and out of the way you should be good to go and remove the casing.









once you have the cover off unbolt the stator and you should be able to pull the main casing off the rest of the motor.





once you get the bottom casing off you will be able to reach down and pull out the drive gears and able to take a look at 2 of your shift forks. now when you pick up the main gear shaft be careful with how you hold it since the bearings will fall right off of it if you hold it upside dawn.. as you can see from this bottom picture i took them out in order after i had the shaft off the engine was able to see the damage done to the gear dogs and well as the shift forks.

ok so your getting into the internals now and you pulled out the main gear shaft without having once of your bearings hit the floor and explode! hold the shaft up by the sproket and IN ORDER start removing the gears and clips. now some of these are going to be down down by pressure clips and you will need a tool to get them spread open and removed. this is what they looked like when i took it off and took all the gears off the shaft.


the pictures below are in order from top left all the way down to the shaft going from left to right and so on and so on




once you have it all in pieces like the pictures above you can inspect your gears and see the wear and why its been pissing you off for so long till you got to this point here are some pictures of the damages to my gears.

1st gear

5th gear

3rd gear

4th gear

6th gear

2nd gear


as you can see 1st, 2nd and 6th has some damage to it and that is what they recoment you replace once you get to this point.. but we are gonna go a little further into this since i will also be replacing 2 of the 3 shift forks since only 1 of mine is in good shape and doesn't need to be replaced.

here are the 2 shift forks that will be getting replaced due to scaring and damage.





in order to remove the shift forks you will need to pull off the shift shaft cover off. remove the shift shaft it self and the shifter stopper lever, once you have all of that out of the way remove the fork shaft cover to remove the forks




pull just the upper one for now and you will see the shaft start to pull out and the forks will slide off when they are all the way out just get them out of the way.

next you will need to pull the clutch basket off the side so you can get to the other gears in order to be able to pull the other shift fork out and see if it needs replacing.

i used an impact run with this one as well and it came right out. hit the boss bolt with the gun if you have one and start pulling everything off. be careful the clutch basket will have rod bearing in them and they slide fairly easy out of the input hole keep everything together so you dont have to buy another bearing for no reason. here is everything in order






once you have the basket off you will need to unbolt 3 more Torx bolts in order to get the bracket that holds the drive/gear shaft in place.




before starting go ahead and remove the bottom shift fork guide pin out just like you did the 1st one and you can start getting the rest out.
once you start pulling that out you will see that the bottom shift fork is going to be a bit of a pain in the ass what i did was start removing everything from the end of the shaft starting with the bearing and putting everything in order untill you can pull off the shift drum. since the last shift fork is on once of the grooves of the shift drum you will just have to work it out a bit.. i used a screw driver to start the shift drum sliding and the rest was easy. takes a little patience and maybe a few cuss words but it all worked out fairly well. and this is the end result








now once you have the shift drum out make sure you take a good look at it to see if there is any damage to it.. if so replace it if not then it can go back in at time of reassembly


that's all i got right now.. i will probably do another one when i reassemble.

if you don't have the service manual yet i suggest you get it because i have also been using it as a guide. and you will need it for torque specs when putting everything back together.


if you need any additional pictures or questions hit me up
Pheonix1001@gmail.com

ill try and help as best as i can.. i know every project has its challenges and its never easy. so ill help with what i can.
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Old 10-07-2011, 12:33 AM   #2
xdonniedarkox
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Very cool thread... Kind of you to fwd the info and effort
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Old 10-07-2011, 02:18 AM   #3
snoman48
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great write up.

Makes me want to go get a blown engine just to tear it apart
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Old 10-07-2011, 07:16 AM   #4
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I picked up a crashed 01 that need a similar tear down. Got it for $250, yes $250! All it needs is a couple pieces of plastic and transmission work for second gear.

99zPheonix1001 I believe there may be a mistake or two in your procedure. You should come and do my bike to make sure the procedure works.

Seriously, thanks for the write up. I'll be using it this winter!

Mark
99 R1
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Old 10-07-2011, 07:00 PM   #5
99zPheonix1001
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lol np... if love to help you but you would have to bring it to Vegas for me to tear it apart.
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Old 10-07-2011, 07:38 PM   #6
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great write-up will be doing this to my spare motor this winter
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Old 10-08-2011, 04:43 PM   #7
snoman48
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Quote:
Originally Posted by Sharksawyer View Post
I picked up a crashed 01 that need a similar tear down. Got it for $250, yes $250! All it needs is a couple pieces of plastic and transmission work for second gear.

99zPheonix1001 I believe there may be a mistake or two in your procedure. You should come and do my bike to make sure the procedure works.

Seriously, thanks for the write up. I'll be using it this winter!

Mark
99 R1

Where the hell did you find that deal?! I'd drive out to Idaho in a heart beat to pick that sucker up
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Old 10-08-2011, 04:57 PM   #8
Benocehcap
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All this talk about the 01R1 1st and 2nd gear going bad got me really nerves!. I have a 01R1 with just 10K on the clock, never got this problem. When should i start seeing this problem?
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Old 10-08-2011, 07:00 PM   #9
Sharksawyer
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Quote:
Originally Posted by Benocehcap View Post
All this talk about the 01R1 1st and 2nd gear going bad got me really nerves!. I have a 01R1 with just 10K on the clock, never got this problem. When should i start seeing this problem?
I've got a 99 with 46,000 miles and never had a problem. I think it's how you treat your bike that matters, not the mileage.

Mark
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Old 10-08-2011, 07:05 PM   #10
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Originally Posted by snoman48 View Post
Where the hell did you find that deal?! I'd drive out to Idaho in a heart beat to pick that sucker up
A year ago, I helped negotiate a deal for the bike for a friend. Picked it up for $700. $400 later, it was back on the road. He rode it for a year and then the transmission went. We put in a clutch thinking it might solve his problem. It didn't so he's selling it to me for $375. I'm pulling the new clutch to save for my 99 so in the end, it's only costing me about $250 Should be able to turn it around for $2k or so. Ca-ching!

Mark
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Old 10-08-2011, 07:33 PM   #11
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I've got a 99 with 46,000 miles and never had a problem. I think it's how you treat your bike that matters, not the mileage.

Mark
i have got a 99 with 40k, i beat it, never thought it would run this long. track, street, wheelies, stoppies... whatever.
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Old 10-09-2011, 02:58 AM   #12
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if you have torn down the motor, why only replace a couple of gears? wouldnt you just replace the lot?
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Old 10-30-2011, 01:38 PM   #13
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if you have torn down the motor, why only replace a couple of gears? wouldnt you just replace the lot?
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Old 11-17-2011, 03:14 AM   #14
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my 99 r1 had this done 3 times in the fist 15000 k's about 3 grand each time and yamaha wouldn't cover it.
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Old 01-26-2012, 10:57 PM   #15
repoman
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fantastic information. Thank you Pheonix, I have my transmission pulled out and now feel confident I can properly inspect and replace what is needed. great stuff.
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Old 12-09-2012, 09:47 PM   #16
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I've got this thing all tore apart......what do I do now?
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Old 01-05-2013, 12:54 PM   #17
Race Engineer
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why would an engine not last 40K, its a jap built engine...
It should mechanically see over 100k with no issue if looked after...it was designed to be revved and its not made of glass, lol....

Makes me chuckle
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