Need Help FZ6 Idle Hunting + Jerking at slow speeds on 1st gear

[helloimnewtobikes]

Hi everyone,

I recently bought a 2006 Yamaha FZ6 with only 18,000 km. It initially ran perfectly, but after a long ride with friends (300–400 km), I started experiencing an issue:

When the engine is fully warmed up, the idle RPM fluctuates by about 300 rpm – for example, between 1020 and 1320 – even though the factory spec is 1250–1300. This does not happen when the engine is cold; cold idle is stable.

Additionally, when riding at very low speeds in 1st or 2nd gear on a light throttle, the bike jerks slightly. I don't feel that this is related to the loose chain as my friend checked it less than month ago and I feel that it's related to this problem as the jerking happens roughly at 1400-1700 rpm ballpark.

What I’ve tried/checked so far: • Replaced the air filter. • Adjusted idle slightly higher. • Took the bike to a shop while changing the rear tire; they found the PAIR hose disconnected and reconnected it. The bike is now a bit quieter, but the issue remains exactly the same. • No error codes or check engine light. • Coolant temperature is always stable (2–3 bars), max 4 bars. • Spark plugs replaced ~2 years ago and <2000 km ago. • Bike is completely stock, no ECU or exhaust mods.

No stalling. Bike starts perfectly and these things apart, runs nice. Or as far as I know - this is my first bike lol.

I also added some red coolant as it has red coolant in the overfill/reservoir tank before our ride with friends and the problem started roughly at the same time. Temperature doesn't raise higher than 4 bars out of 6.

Tried the diagnostics and when throttle position is off it's 16 and at max it's 101. Does this outrule the faulty TPS? I have read that even some 2006 models were recalled. My model is RJ07 (or FZR-RJ076/600).

Has anyone had a similar problem on an FZ6, and what was the fix? I’ve read about possible causes such as TPS issues, vacuum leaks, throttle body sync, or a dirty Idle Air Control Valve, but I’d like to hear from people who have solved it. Is this due to the ignition / air / fuel?

I have uploaded the video of the hunting RPMs. I'll another one where I walk around the bike to capture better the overall situation better.
Thanks in advance for any advice.

 

[Gary in NJ]

It could be as simple as dirty throttle bodies or maybe they need to be synchronized.

 

[helloimnewtobikes]

It could be as simple as dirty throttle bodies or maybe they need to be synchronized.

Thanks for the reply! So how would I clean the throttle bodies? The gas tank is empty right now so it would be easy to do at the moment.

The sync I would leave to professionals, because I don't need specific tools. I have the Haynes Service & Repair Manuals and it pointed out same things as you:

"If a smooth, steady idle cannot be achieved, the throttle bodies may need synchronizing (see Section 4). Also check the operation of the fast idle unit and examine the intake manifolds for loose clamps and cracks which will cause an air leak, resulting in a weak mixture."

First of all, what is fast idle unit and can I spray something to spot the possible leaks? What should be sprayed?

 

[Gary in NJ]

With a warm stopped engine, open up the airbox and the top of the four throttle bodies will be visible. Remove the air filter. While holding the the throttle wide open, spray carb cleaner into the throttle bodies. Allow a few minutes for the cleaner to dry and then start the engine. Expect a rough start and some smoke while the engine consumes any remaining cleaner. After it is running well (hopefully with a steady idle) reassemble.

 

[helloimnewtobikes]

With a warm stopped engine, open up the airbox and the top of the four throttle bodies will be visible. Remove the air filter. While holding the the throttle wide open, spray carb cleaner into the throttle bodies. Allow a few minutes for the cleaner to dry and then start the engine. Expect a rough start and some smoke while the engine consumes any remaining cleaner. After it is running well (hopefully with a steady idle) reassemble.

Thanks Gary!

So no need to wipe the residuals with a cloth - just a spray is enough?

I’m going to shop buy TB cleaner - might also grab also the Motul Injection Cleaner and fill the tank with it. The previous owners rode just under 1000km within 2 years…

I hope these would solve the issue. Otherwise, I’ll take the bike to service to sync the TBs and for inspection.

 

[helloimnewtobikes]

Update to the jerking: when driving on 1st gear, for example, 12km/h and the RPMs around 2000 the bike jerks/nudges back and forth a little bit, despite my hand being steady on the gas.

Are these two issues related or can this be due too loose chain? Or what are the symptoms of faulty chain?

E: I feel it's strange that the jerking/nudging happens only in certain RPM bandwidth.

 

[TownsendsFJR1300]

It's cheaper to buy the TB sync tool than to pay a shop:
https://www.carbtune.com/ and do it yourself...
It'll quickly pay for itself..

They tend to F..k things up IME.

As for the chain, I've found it CRITICAL to have it clean, lubed and set at EXACTLY 2":


My shifts were getting sloppy and I found the chain needed SLIGHT adjustment, 1/4 turn outwards, tightening
the chain 1/4" up and down.. MUCH, much better...

.

 

[Gary in NJ]

It's cheaper to buy the TB sync tool than to pay a shop:
https://www.carbtune.com/ and do it yourself...
It'll quickly pay for itself..

They tend to F..k things up IME.

True. A shop is trying to get it done as quickly as possible…close enough is good enough. Where as when it’s your bike, it’s not done until it’s perfect.

 

[TownsendsFJR1300]

Before I bought mine in 2004, I had to pay (Yamaha shop) for a sync on my '04 FJR as I was having some running issues.
The bike was under warranty. They "synced" the bike and couldn't find / fix the issue.

I found the issue, a corroded connector under the tank and re-checked their sync work.

On the Gen 1 FJR it has air screws like the FZ6 (and should be synced the same) however
being a 4 separate TB engine, there are screws to sync the "main shaft". These are painted with white paint from
the factory and NOT MEANT to be adjusted.

This dealer ADJUSTED one of these screws as you could see the main broken and the screw adjusted about 1/4 turn.
I suspect they did this as THAT screw was easier to adjust than getting to the AIR SCREW.

I had to re-set that screw to the factory spot and properly sync..


IE; Do it YOURSELF and know what's been done..


BTW, the Carbtune was cheaper than the messed up sync I paid top dollar for
at a dealership...

 

[helloimnewtobikes]

Thanks Gaey

Before I bought mine in 2004, I had to pay (Yamaha shop) for a sync on my '04 FJR as I was having some running issues.
The bike was under warranty. They "synced" the bike and couldn't find / fix the issue.

I found the issue, a corroded connector under the tank and re-checked their sync work.

On the Gen 1 FJR it has air screws like the FZ6 (and should be synced the same) however
being a 4 separate TB engine, there are screws to sync the "main shaft". These are painted with white paint from
the factory and NOT MEANT to be adjusted.

This dealer ADJUSTED one of these screws as you could see the main broken and the screw adjusted about 1/4 turn.
I suspect they did this as THAT screw was easier to adjust than getting to the AIR SCREW.

I had to re-set that screw to the factory spot and properly sync..


IE; Do it YOURSELF and know what's been done..


BTW, the Carbtune was cheaper than the messed up sync I paid top dollar for
at a dealership...

Thanks Gary and Newsends,

Now I’m interested into buying one of those.

Is it hard to use? I have the Haynes manual, but this is my first bike and I haven’t repaired our hands by myself - the last time I really got my hands dirty was when I was 16 and riding my 2-stroke Yamaha DT. Still miss those days.

E: I almost forgot to answer to the original problem - the rough idle and jerking.

The chain was fine- Haynes manual says the ”slack” should be between 45-55mm and it was 50mm. I might need to replace them all soon, as they never been changed before (20tkm).

Previous owner drove only 100km or so during almost two years. He bought it during pandemic and eventually the bike stood in the garage for most of the time. The solution was to buy the Motul Boost and Clean, fill the thank with 98E5 (as always) and have a great ride with my bois. Gave the bike the old good high rev treatment. Both the jerking disappeared and idle stays 1260-1320 when engine is warmed up. So I drove another tank with only 98E5 and repeated the procedure. Now it keeps strange tic-tic-tic sound, but it’s probably just Yamatick. I’m starting to overthink these things.

After above mentioned procdure it seems best to change the oil as last oil change was done 11months / 2300km ago. I’m going to go with full-synthetic 7100 10W-40. Somebody told me that these additives may leak some shit into the oil and it’s adwised to change the oil soon. Sounded strange but only thing I know about bike is: change the oils often and use quality products.

Btw, bought an HF airfilter and changed it. Is the seal supposed to be coming off from the filter when holded in hand or is it supposed to be like OE filter where the seal is always solid? One of my friend said that that does not sound good and it may be defaulted and should be replaced as it can lead dirty air flowing to the engine.

 

[TownsendsFJR1300]

PM sent re syncing

Newsends




.

 

[helloimnewtobikes]

PM sent re syncing

Newsends




.

Apologies Scott (?),I got your nickname totally wrong

 

[TownsendsFJR1300]

You have mail!


.

 

[helloimnewtobikes]

You have mail!


.

Got it, appreciate your help!!

 

[grahammarsden]

The idle does sound a bit rough, have you checked the spark plugs?

I know you say they were replaced 2 years and not many miles ago, but if there's any build up or soot etc on them it could indicate another issue.

 

[helloimnewtobikes]

The idle does sound a bit rough, have you checked the spark plugs?

I know you say they were replaced 2 years and not many miles ago, but if there's any build up or soot etc on them it could indicate another issue.

I was lazy and poured Motul Boost & Clean additive into the tank and drove like a maniac for a while. Solved the problem and rpms stay in the 1260-1320.

Is it worth taking the radiator away and check/change the spark plugs? I was wondering if it’s worth swapping then for Iridium plugs?

Furthermore, maybe also clean the coils inside with adequate cleaner?

 

[TownsendsFJR1300]

I have and like the iridium's. In there probably 10 years ago..

I was able to R & R them W/O removing anything.
Tight, but do-able (and I have somewhat large hands)

 

[tuning-forks]

I did not remove the rad but I undid the mounting bolts so I could push it away a bit for the plugs that were more difficult to get to. And loosened the plastic zip-tie holding the hose tight by the coolant recovery bottle.

 

[grahammarsden]

I was lazy and poured Motul Boost & Clean additive into the tank and drove like a maniac for a while. Solved the problem and rpms stay in the 1260-1320.

Is it worth taking the radiator away and check/change the spark plugs? I was wondering if it’s worth swapping then for Iridium plugs?

Furthermore, maybe also clean the coils inside with adequate cleaner?

You can check the plugs without draining the coolant and removing the radiator by undoing the radiator bolts and carefully moving it a little bit forward to give you more space.

Then use the hinged tool from the kit under the seat to take the plugs out and see if they're in good condition.

Regarding changing the plugs to iridium, honestly I doubt you'd notice a difference (apart from the price!)

 

[tuning-forks]

Regarding changing the plugs to iridium, honestly I doubt you'd notice a difference (apart from the price!)

More or less cost? I'm assuming it may depend where you are and what you are comparing to. The stock EK (double ground element) plugs are more expensive than the EIX (iridium) where I am.
Both are substantially more than the generic CR9E plug (non-stock).