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Discussion Starter · #1 ·
Recently had the engine on my 04 r6 apart to replace the output shaft and ended up lapping one of the intake valves after I found out it was leaking. Got it all back together and had to reshim the valve that I lapped, so all valve clearances were ok. Cam timing looked perfect before I put the valve cover on. The bike runs but it seems like cylinders 3 and 4 are misfiring. The headers do still get hot for those cylinders but not nearly as hot as cylinders 1 and 2. Tried swapping the coils with the coils from cylinder 1/2 with no luck so I doubt its a coil issue. Has brand new plugs, CR10EK which is what it had before I took the motor apart. Could the fuel injectors be clogged from sitting so long without any fuel in them? The bike has a new air filter too so I know it’s not that. Above 3k-ish rpm it sounds fine but below that sounds like a Harley. I have a lot of experience working on bikes but just can’t figure this out any help would be appreciated. Bike ran great before I took it all apart. The bike also has Mitsubishi coils, not the recalled denso ones.
 

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Discussion Starter · #3 ·
Throttle bodies synced?
Each cylinder registers within a percentage of each other with compression testing?
Haven’t compression tested it yet I’ll do that soon, I don’t see why the compression would be any lower when it used to run good though. Valves are in spec and I made sure all the valves seal before I put the head back on so I don’t see any reason for compression loss. I’ll test it to be sure tho I’ll pick up a compression tester tomorrow
 

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Sometimes I forget to start simple. Pull the plugs to see if they got fouled or dirty, also check gap because if the gap is off or tips bent slightly they can miss
 

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Discussion Starter · #5 ·
Sometimes I forget to start simple. Pull the plugs to see if they got fouled or dirty, also check gap because if the gap is off or tips bent slightly they can miss
Will check that when I pull them to do the compression test later today, but like I said they are literally brand new so idk why they would have problems. Could clogged injectors be a possibility from sitting so long?
 

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Discussion Starter · #6 ·
Just did a compression test, I got exactly 150psi cold on every cylinder (about 30 degrees outside right now). That’s way below spec (190-240psi is the spec I believe) so I really hope it’s just my tester not being accurate. When I had the head off the cylinders had perfect crosshatching on them, didn’t see any signs of wear at all so idk what’s up with that. Aside from the low compression readings, compression is definitely not a problem for cylinders 3 and 4 as it has the exact same compression as cylinders 1 and 2, which didn’t misfire at all. My battery is a bit low by the way, so it cranks a bit slow, could that cause the low compression readings? Anyways, compression is clearly not causing the misfire here, any other ideas?
 

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I wouldn't worry about it. They're even. That's what matters most. You can add oil to the cylinders and re-test but I'd just move on. There's a ton of valve overlap so even a normal crank speed I suspect will produce low readings.

Are you familiar with the throttle body sync I mentioned? Basically you're checking to make sure each throttle body is producing the same amount of vacuum at various RPMs. Unless those screws have been toyed with already you should be good there, given the fact that cylinder compression is even. But procedure dictates that we check that post valve lash adjustment.

Calibrate your auto-choke...

.
 

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Discussion Starter · #8 ·
I wouldn't worry about it. They're even. That's what matters most. You can add oil to the cylinders and re-test but I'd just move on. There's a ton of valve overlap so even a normal crank speed I suspect will produce low readings.

Are you familiar with the throttle body sync I mentioned? Basically you're checking to make sure each throttle body is producing the same amount of vacuum at various RPMs. Unless those screws have been toyed with already you should be good there, given the fact that cylinder compression is even. But procedure dictates that we check that post valve lash adjustment.

Calibrate your auto-choke...

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Thanks, I was really worried about the compression, the compression was a bigger deal to me than the misfiring. I dont think my throttle bodies need to be synced. I havent messed with the adjustment screws and i dont think the previous owner has either, like i said the bike used to run fine so all should be good there. When i took the spark plugs out to do the compression test I noticed that they were all wet with gas. Not completely soaked but there was a pretty noticable amount on each plug, making me start to think it is a spark issue. The engine would also flood very easily on cold starts, which surprised me, since i never had the engine flood out on me before. If I started it up and revved it a couple times, it would die out and not want to start again unless i waited 30 min or held the throttle wide open while cranking. This happened 2 times. I think i'll double check the cam timing while i still have the throttle bodies off, put the old plugs back in it, and disconnect the power commander tomorrow and see if anything changes. I did check the spark though and got a consistent blue spark on all coils/plugs, so im pretty confused. Any other ideas?


edit: One more thing, I noticed when i first start it up, itll sound like its running on 4 cylinders for a bit but the second i rev it it goes right back to sounding like a harley.
 

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If you have a compression problem the chances of all 4 being dead on each other is slim to none. I highly doubt thats an issue. With the plugs being wet you could always replace them as its cheap maintenance and then you know you got fresh plugs in. However with them being wet im wondering if it isn’t something like the power commanders fault. Using a map table and dropping in far too much fuel for a cold start. Let us know how it acts after taking off the power commander.

or wait instead of taking it off. Just plug into it and load up a zero map. With that loaded it doesn’t change any ratios pluged in by ecu
 

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Verify your fuel pressure and check your grounds.

If you had the butterflies closed when you checked compression your reading is off, so it's no big deal.
 

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Discussion Starter · #11 ·
Verify your fuel pressure and check your grounds.

If you had the butterflies closed when you checked compression your reading is off, so it's no big deal.
Throttle bodies were off when I did the compression test. Will check the grounds later today and try to verify the fuel pressure.
 

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Discussion Starter · #12 ·
With the plugs being wet you could always replace them as its cheap maintenance and then you know you got fresh plugs in
The plugs are brand new though. Also one thing I noticed is, while cylinders 3 and 4 are both misfiring, it seems like 4 is the worst. Cylinder 3 gets way hotter than 4 but still not even close to as hot as cylinders 1 and 2.
 

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................ When i took the spark plugs out to do the compression test I noticed that they were all wet with gas. Not completely soaked but there was a pretty noticable amount on each plug, ........... engine would also flood very easily on cold starts, .............. started it up and revved it a couple times, it would die out and not want to start again unless i waited 30 min or held the throttle wide open while cranking. This happened 2 times. .................
A lot of this sounds familiar; though there are some differences. What state and region are you located? I'm in Southwest Ohio. When it ran, how did it perform on a cold engine, say at 110F versus 160F?

Any other changes besides the power commander, such as block-off plates and exhaust? You may have already stated but just remind me.

Sounds like you will require a tune. Disconnecting the Power Commander is a good troubleshooting step. The Winter fuel blend here requires that I make some tweaks.
 

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Discussion Starter · #14 ·
A lot of this sounds familiar; though there are some differences. What state and region are you located? I'm in Southwest Ohio. When it ran, how did it perform on a cold engine, say at 110F versus 160F?

Any other changes besides the power commander, such as block-off plates and exhaust? You may have already stated but just remind me.

Sounds like you will require a tune. Disconnecting the Power Commander is a good troubleshooting step. The Winter fuel blend here requires that I make some tweaks.
I'm in northeast illinois. Before i had it all apart it ran fine even cold. Throttle response would be a little sluggish until 130f since thats when the automatic choke turns off but other than that it ran fine never misfired or gave me problems. Other than the power commander I have slide stops, homemade block off plates, BMC air filter, and I just recently put a shorty yoshimura trc on it. Exhaust before that was a yoshimura rs3 i believe, not sure on the exact model it was just like a 2ft long carbon yoshimura. I'm sure the tune is way off on it, I never had it mapped and since i bought the power commander used its running whatever map the bike it came off of had. But it ran fine before so i dont see what would've changed with the tune. I will still try disconnecting it and see if anything changes. Didn't get a chance to work on it today since i was busy cleaning up my garage, but i'll try whatever i can think of tomorrow. Planning on putting the old plugs back in, swapping coils 3/4 with 1/2, going over all the connections in the wiring harness, disconnecting the power commander, double checking cam timing and doing another compression test while the engine is warm. I can post a vid on how the bike sounds if that would help at all, but its nothing special just sounds like any other misfiring r6 on youtube.
 

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Putting a power commander on using mapping from a previous bike the power commander was on defeats the whole porpoise of having the power commander. You would be better off taking it off until it can be installed with a proper tune. I wouldn’t doubt if your bike runs fine once it’s removed. Also try your old plugs. Perhaps you have a set of knock off or a bad set of new plugs. I’m going to say this is most likely just a tuning issue.
 

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Yeah bike is fine. Just needs tuned with all the changes. If you ride during the Winter, make sure it's tuned on Winter fuel; assuming your area switches like much of the nation.
 

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Discussion Starter · #17 ·
Just got it all back together and started it up with the old plugs and switched coils. Bike was running fine until it warmed up a bit. Headers on 3/4 were way hotter than before but still not as hot as 1/2. Once it got to about 120f I revved it a bit and it started misfiring again, and the cylinder 4 header cooled down a lot. Cylinder 3 header seemed to stay the same. So it seems like the issue starts after it warms up.
 

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Check the spray on your injectors. Verify fuel pressure. Spray carb and choke cleaner around the throttle bodies and see if the revs creep.
 

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Just got it all back together and started it up with the old plugs and switched coils. Bike was running fine until it warmed up a bit. Headers on 3/4 were way hotter than before but still not as hot as 1/2. Once it got to about 120f I revved it a bit and it started misfiring again, and the cylinder 4 header cooled down a lot. Cylinder 3 header seemed to stay the same. So it seems like the issue starts after it warms up.
Did you take the power commander off?
 
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