#2 Cylinder missing - only 6400 miles

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tamarack

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Been a lurker for a while now absorbing all the info on the site prior to purchase and post purchase. Now to ask a question. I've seen similar issues listed before but not quite exactly the same as mine..as far as I can tell anyway....the details.

Purchased a 2007 in February with 5700 miles on it. I now have 6400 miles. Bike is stock. Here is what's happening. The number two cylinder, and sometimes the number 4 is missing. It happens the most often, and most severe when cold but also happens at any steady speed/RPM. It is more noticable at lower RPMs (4000 and below). It has been slowly getting worse. When dead cold for about the first 30 seconds to a minute I can hear either a “clunk” sound when it misses or it could possibly be a small “backfire” into the air cleaner. Not sure if it's either one of these but that's what it sounds like. Here is what I've done so far..mostly thanks to info gathered on this site.

1. I called Yamaha and they told me the ignition switch and ground wire recalls recalls were performed. But I'm not really sure to tell if this is true or not.

2. I've run two tanks of Sea Foam. (On the third) I did this because no telling how long it sat at the dealer, or the previous owners garage before I purchased. However I've noticed no change with the Sea Foam.

3. Changed the spark plugs. (The replaced plugs looked fine and no noticable difference between them)

4. Performed a TBS. All cylinders were in spec but I adjusted them to all equal.

I found out what cylinders where missing when the manometer was attached to throttle bodies. The number two cylinder would randomly but frequently (about every 30 seconds) go from 25 cm to 0 then back up to 25. The number 4 cylinder would do the same but only once to every 4 or 5 times of the number 2.

As mentioned it's getting slowly worse and starting to get to the point where I'm concerned I may be doing some real internal damage. Any thoughts, ideas and suggestions will be welcome. I really don't want to take it to the dealer.

I apologize if this is the same issue that's been discussed to death but from what I've seen before it hasn't been discussed, or I couldn't find a discussion dealing with a specific cyclinder. Just a “hesitation.”

Any reply's will be welcomed. Hopefully one day I will be able to contribute answers instead of questions.

 
Two things to ask to help clarify....

1 - Does this "missing" also happen when the bike is completely warmed up, i.e., when the temp gauge is showing 4 bars?

2 - What is your idle speed set at?

Reasons for questions.....FJRs are notorious for "missing" and "clunking" during warm-up. It's pretty much a given to NOT attempt to diagnose ANYTHING on an FJR until it's fully at operating temp. Second, FJRs are also notorious for coming from the factory/dealer with the idle speed set too low. It really should be 1100rpm when fully warmed up.

Let's start with the basics and go from there, okay?

 
Two things to ask to help clarify....

1 - Does this "missing" also happen when the bike is completely warmed up, i.e., when the temp gauge is showing 4 bars?

2 - What is your idle speed set at?

Reasons for questions.....FJRs are notorious for "missing" and "clunking" during warm-up. It's pretty much a given to NOT attempt to diagnose ANYTHING on an FJR until it's fully at operating temp. Second, FJRs are also notorious for coming from the factory/dealer with the idle speed set too low. It really should be 1100rpm when fully warmed up.

Let's start with the basics and go from there, okay?
 
Thanks..To answer questions.

Yes still missing when completely warmed up but not nearly as noticable. Although I do not hear the "clunk" noise after about a minute after initital start.

(It was completely warmed up when I had the Carb Tune hooked up) I can steel feel it and see the tach drop when at a steady RPM/Speed.

The idle is at 1000 to 1100 when warm. (It varies a little)

I didn't check all the spiders but did check all electrical plugs I could see, and pull apart, while the tank was up. This was only three that I could open but they were clean.

 
Sorry to hear about your problem. Here are some links to look at regarding your Spiders and possible shorts:

https://www.fjrforum.com/forum//index.php?showtopic=126635

Here to see if your Coil(s) are Shorting:

https://www.fjrforum.com/forum//index.php?showtopic=126721&st=0&p=714281entry714281

https://www.fjrforum.com/forum//index.php?showtopic=125763&st=20&start=20

Good Luck with your fix...
Thanks for the links. I tried looking for detailed pics/loactions of all the spiders but could not find it until now! I guess if those don't solve It's time to learn more about the bike sooner then I wanted...

 
I would start by checking the spark and compression on all cylinders. You can check the spark with a timing lite. Just look at the lite while it's hooked to a wire and watch the spark. You will be able to see a random pattern on a missing cyl. When checking the compression remove all plugs, ground all wires, hold the throttle wide open while cranking. Comp should be between 195-255, and no more than 14 psi difference between them all.

If you are seeing the manometer jumping around on those 2 cyls, that usually means valves leaking. It could be they are too tight or carbon build up. If you see those cylinder are lower on compression then you can do the shock treatment of Ring Free. The shock treatment is one 12oz bottle per tank for 4 tanks. That should clean out the carbon, but if you still have low comp then the valves may be too tight.

 
From what I am understanding from your description is that the cylinder 'drops out" intermittently. This is more symptomatic of an electrical issue rather than a mechanical problem. This is further supported by the fact that #4 cylinder will also drop out on occasion.since both #2 & #4 cylinders use the same coil.

Since the bike has sat for a while I would start by looking at the ECU connector for signs of corrosion before you start tearing the bike apart. Also check the spark plug lead connection to the spark plug boot. These are the easy things to check. Go to the Brodie harness thrrad and check the condition pf the spoders ( I think you can check 8 of them). Everything else will requie the removal of plastic .

 
From what I am understanding from your description is that the cylinder 'drops out" intermittently. This is more symptomatic of an electrical issue rather than a mechanical problem. This is further supported by the fact that #4 cylinder will also drop out on occasion.since both #2 & #4 cylinders use the same coil.

Since the bike has sat for a while I would start by looking at the ECU connector for signs of corrosion before you start tearing the bike apart. Also check the spark plug lead connection to the spark plug boot. These are the easy things to check. Go to the Brodie harness thread and check the condition pf the spiders ( I think you can check 8 of them). Everything else will require the removal of plastic .
Gen II's have cylinders 1&4 and 2&3 on a common coil.

There are many posts regarding low RPM drivability issues for the early Gen II's and I'm starting to think they are sensitive to electrical issues and/or are susceptible to corrosion. Now that they have been around a few years minor corrosion maybe starting to build to a point where it's becoming problematic.

Link to my own recent stumbling adventure. I've had only a couple minor re-occurrences since cleaning bat terminals.

 
From what I am understanding from your description is that the cylinder 'drops out" intermittently. This is more symptomatic of an electrical issue rather than a mechanical problem. This is further supported by the fact that #4 cylinder will also drop out on occasion.since both #2 & #4 cylinders use the same coil.

Since the bike has sat for a while I would start by looking at the ECU connector for signs of corrosion before you start tearing the bike apart. Also check the spark plug lead connection to the spark plug boot. These are the easy things to check. Go to the Brodie harness thrrad and check the condition pf the spoders ( I think you can check 8 of them). Everything else will requie the removal of plastic .
I also thought of a coil, but according to the FSM one coil fires cyls #1 the other coil fires cyls #2. I doubt both coils or there connections are going bad.

Also if a cylinder doesn't fire it will still create vacuum, unless there is a mechanical problem.

A spark problem is easy to diag with a timing lite, and will save a lot of time chasing ghosts.

You can check the compression and spark by simply raising the tank. If all that checks out then start chasing.

my .02 cents

 
Did ya happen to think of maybe calling the fuzz an filing a missing cylinder report?

Fuk dood ,what did you do to make it depart?

With that kinda mileage, If you was sexual with it ya might wanna hide.

 
Thanks all. Different opinions different things to check. I will start out with the simple and progress from there. Battery cables, Spyders, compression, ECU. I will keep updated as I will be working on it this weekend.

 
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