please help - 03 R6 problems between 4000 and 8000 RPMs

[speedyafrica]

hey guys, some help diagnosing the problem would be greatly appreciated.

problem: i have had my 2003 R6 since january 2011 and it's been my daily driver since. i recently noticed that when my RPMs are between 4000 and 8000, the bike feels jerky / hesitant. it feels almost as though someone is constantly letting go of the throttle a bit, and then opening it, and letting go repeatedly. i have been riding for 3 years with my bikes being my only transportation, and ive had this one since 2011, so i know its not my thottle imput causing this. any ideas on what to check???

what i have done so far: i have been keeping up with the oil changes every 4000 miles or so. i always put 93 in at the pump, and a little injector cleaner every 4th fill up. i keep my chain well lubed, and just last week did a 520 conversion with stock sprocket teeth, so new chain and sprockets. i also have a BMC race air filter, and a hindle slip-on exhaust. power commander III with the map for a hindle slip-on with aftermarket filter. new NGK spark plugs 3 weeks ago, and checked to make sure i have the new coils (not the recalled ones). i cleaned my TPS (throttle position sensor) 2 days ago, so the throttle is a tiny bit more responsive, but the jerky/hesitation is still there and has been for about a week now. i also followed the how to thread on synchronizing the throttle bodies (so monometer is built and carbs sync'd). they were pretty far off, but they are now within half an inch at operating temperature. i also checked the engine diagnostics after i cleared them, and they are clean.

possible causes?? : i am taking my bike for a valve adjustment next week, since it has about 42 000 miles. could this be the cause?
i have also read that it could be the fuel pressure regulator, in which case i am going to buy a used throttle body and airbox from the 2005 R6 and swap them since they are a tiny bit bigger and they dont have the same fuel pressure problems. since i can get both of those together for less than just a new pressure regulator, i figured why not.

i am really not sure what else it could be. sorry for the long post, but i tried to be as thorough as possible.

again, any help/advice would be greatly appreciated. thanks

[speedyafrica]

ok, so since the last post, ive done some things to try and solve the jerky/hesitation problem it has been having with NO LUCK

the problem however has changed since then... now the bike has the jerky/hesitation only in 5th and 6th gear but throughout any RPMs.
[whereas before it was in a certain RPM range in any gear]

here is what i have done so far in addition
- replaced the entire throttle body assembly (including TPS sensor, fuel regulator) with an 05, which is slightly bigger and an 05 air box to match.
- i had the valves checked and none of them needed any adjustment.
- i also replaced the fuel pump

i wish it didnt have to come to this, but it looks like i will just be riding my bike as is until the problem either becomes more pertinent to show me what is wrong, or until something breaks so i can fix it. if anybody has had this happen or have any further ideas, PLEASE let me know. i do not want to spend any more money replacing things until i know what the problem is - if it keeps going like this, i will have replaced the entire motorcycle before i find the problem.

any ideas?? thanks guys and gals

[speedyafrica]

update-

so i got the jerkyness to stop completely - it was the timing chain that needed to be replaced. when the shop took the old one out, it did not seem to be stretched at all, but the went ahead and put the new one in anyway and no more jerkyness. its most likely that somehow just one or two of the timing chain links stretched and not the whole chain in this case.

[MELK-MAN]

Originally Posted by speedyafrica

update-

so i got the jerkyness to stop completely - it was the timing chain that needed to be replaced. when the shop took the old one out, it did not seem to be stretched at all, but the went ahead and put the new one in anyway and no more jerkyness. its most likely that somehow just one or two of the timing chain links stretched and not the whole chain in this case.

When a cam chain has a bunch of hours on it, the cam sprocket will be rotated slightly. 1 forward, 1 back a bit. timing marks won't line up exactly. But you don't get "1 or 2" links that wear. they all wear over time, and yea, with 42k on the bike, that chain was a good amount longer than it was when new.

Also, when stretched that much, the cam chain tensioner is extended way out. If it was at the end of it's range, it would have left the cam chain slightly loose. THIS causes changes in the actual cam timing when holding steady throttle, and hence your issue.

so kind of blind luck that this issue got solved! Sometimes it's better to be lucky than good. glad ya got it sorted, but sad you threw a bunch of parts at the bike.

[speedyafrica]

See that is the thing that I dont understand, and the shop didn't either. When they opened the engine to take the old timing chain out, it wasnt stretched at all, and the tensioner was not fully extended. It was the same length as the new one they were replacing it with.

Unfortunately it also recently started making an awful noise that does not seem to be coming from the right side of the engine where the timing chain sits, and where the noise was coming from before. It started yesterday on my way home from school. I have a short audio of what it sounds like that I will add to this reply. I am scared to drive it at this point and do not know what is wrong.

Any further assistance will be greatly appreciated since this is my daily driver.

[Ryan5544]

That sounds real nasty. Does it go away shortly after starting it, or does it just keep knocking away?

[speedyafrica]

It actually has been there very softly since ive had the bike, which I knew wasnt normal, but it was the same as a lot of people have, and a lot of their responses were always, well yamaha has noisy engines. The last 1000 miles around town it has been getting worse little by little. Since it was so soft, even the shops around here couldn't diagnose it and said its one of those thins that I will probably have to wait until it gets worse before I could see where the problem is.

However, when I rode it home yesterday, the loudness of the noise more than tripled . It hasnt stopped since, and the bike was definately warm when i got home (~210 °F). I didnt drive very fast once it started being that loud.

[MELK-MAN]

so is the herky-jerkyness gone, or is it still doing it? i can't unzip that file from this computer..

WOW>. ok. heard that. It almost sounds like a shim came out when they shimmed the valves. when that occurs, there is a tremendous amount of clearance between the bucket and the cam lobe. That is kind of what that sounds like. espeically if it does it consistantly with rpm, not so much with how much load is on the motor. But since you didn't have valves adjusted that does not seem likely. Also, doubt that is the case since you say it just started doing it worse and worse.
very hard to say what that noise is.
How about checking shift shaft where it goes into the motor.. make sure the circlip that holds the shift shaft where it goes itnot the motor on the left side, didn't come out of the groove and allow the shaft to move inward. When it DOES, the back of the shift shaft (about 1' long) rubs against the back of the clutch basket and makes a sound like a bad valve. I had this occur once, and we pulled the head off the bike before figuring out what had occurred

listening more, that doesn't sound like the issue either.. that sounds pretty bad.

[speedyafrica]

The herky-jerkyness disappeared when I replaced the timing chain (that didn't look stretched at all) and has not came back since.
The sound has been there very faintly for a long time, but just in the last few thousand miles started getting louder. And like I said before, it started getting really bad, like it is now, just yesterday.

I will check the shift shaft tonight, just in case, but I don't know where else to start looking. I also just found out that the local shop wont even be able to take a look at it for another 2 weeks if I could somehow manage to get it there tomorrow. Since its my daily driver, I am kind of stuck in between a rock and a hard place at the moment.

I do appreciate your insight so far a lot, thank you.

[MELK-MAN]

are you sure the cam chain tensioner isn't failing?? sounds like some issues were resolved, but some got worse after the new cam chain was installed. you can removed the right side timing cover and tug on the cam chain from there. if it's reasonably tight against the cam chain guide, that isn't the problem.