Can't diagnose the cause of a misfiring cylinder

Hello guys, I can't diagnose the problem with a misfiring cylinder (it's cylinder number 2). It only fires when the choke is on. The bike is 1997 Yamaha XJ600S Diversion, British version.

The story with this bike's problems is pretty long but here are the crucial symptoms/information:
-the jets have been cleaned
-no problems with spark plugs and almost certainly no problems with coils (with swapped coils #1 and #4 were working perfectly - normally #4 misfires WITH CHOKE ON but it was running with choke when the coils were swapped - and #2&#3 were not working at all)
-valve clearances and the state of valves in general are unknown as of today
-the pressure in the cylinders is about 0.8 MPa, not very high but enough for them to work
-spark plugs #2 and #3 are way darker than 1&4
-the strangest thing with this problem is that only THIRD cylinder was misfiring before I cleaned the pilot jets. I believe that when I started it after cleaning the pilot jet of carb #3, cylinder #3 started working but at the same time cylinder #2 stopped!

My ideas are that the intake valve could be bent, the clearances could be way off or the pilot screw needs to be adjusted (I did not adjust, take apart, or clean these when I was cleaning the carbs).
What do you think?

 

You should check the valve clearances and do a compression test with the throttle full open first.

 

And after that clean the blocked idle circuit passages. The idle mixture screw needs to come out, and you might need to replace the o-ring that's in there too.

Do the easy and inexpensive things first.

 

.8Mpa is equivalent to approx. 116 psi, not the best compression ,but should be enough to run reasonably well

 

Thanks for your replies,

How big do you think is the chance that I'll have to replace the valve cover gasket that's been sitting there for more than 10 years once I open it? I'll probably need to open it anyway but just want to know how likely is that I'll have to add that to the budget.

How do I make sure the whole idle circuit is clean? This might be a dumb question but do I just stick a tiny cord into it and move it in every direction hoping for some dirt to fall out or blow some compressed air into its ends...?
Also isn't it like the mixture is too lean anyway so if the clog was somewhere on the side of the mixture screw it'd rather limit the air intake making the mixture richer and thus the symptom of only running on choke couldn't really appear?

 

The idle circuit consists of more than one drilling, so you can't put a wire through it as the wire can't go around the sharp angles.

If the idle passage is clogged then it won't get any fuel into it no matter how clean the idle fuel jet is. The idle mixture screw meters both fuel and air, the air providing the motive force that allows the fuel to get sucked out of the float bowl. Turning the enricher (choke) open is how the cylinder is getting fuel at idle.

https://www.xjbikes.com/forums/threads/in-the-church-of-clean.14692/

https://www.xjbikes.com/forums/threads/clean-your-own-carbs-the-whole-9-yards-by-rick-massey.2908/

http://www.xj4ever.com/inside your carbs.pdf

 

Check the vacuum hose that runs from the #2 carb boot to the vacuum petcock. If that is loose or has a leak it will cause a misfire on #2 but fire when the choke is on.

 

Regarding the valve cover gasket it depends on its condition but I would change it if it was my bike.

 

But the vacuum hose runs from #1 carb boot, not from #2

 

Does your bike have a fuel pump because the carburettors are above the tank. Is it low fuel pressure?

 

Yes it has, however recently all of the testing was being done without tank, just sucking the fuel from a canister. I don't think the problem lies there.

Also maybe it's worth mentioning that sometimes the pilot air jet and the main air jet are full of fuel. I'm not sure if it should be like that.

For now I'm gonna make sure to clean carbs properly & check valve clearances. Meanwhile, if anybody has other ideas I'll appreciate if you post them ITT.

 

I think they are downdraft carburettors on your machine. Yes do the clearances first. They have to be correct because you will eventually balance the carburettors to the vacuum of each cylinder. You want them opening and closing at the right time.

 

Check all of the vacuum port caps for cracks though.

 

For anyone wondering: the carbs weren't synced properly. I used feeler gauge to sync them when off bike cuz I thought that I'd better fix the misfiring issue first and then sync them properly... stupid me.
Thanks for all your help guys