What a PITA. 
First, I suggest assume nothing. New spark plugs can fail, cleaned carbs can still have bits of crud which get dislodged after a few hundred kms use - particularly if you've used all the power!
I'd start by pulling each plug cap in turn to see if the misfire is electrical - ie, plug, plug cap or plug lead.
If you can't pin it down to electrics, start by taking the carb tops off to check that the needles and diaphragms are OK.
Check the fuel filter.
Check the air filter and the air intake.
I don't think it's EXUP-related as a stuck/misaligned valve won't cause those symptoms.
Check electrical connections and earths. Take a close look at the multi-pin connector under the left side of the tank - the one in the rubber boot that you would have moved doing the Ivan's installation.
You are probably thinking to pull the carbs straight away but eliminate other possibilities first.
Good luck! 
Thank you so much for this thorough reply which gives me a direction forward.
Just to be clear (as I have never done this before, I'm quite okay at following instructions -> installing Ivan, checking valves but I lack experience) when I pull the individual spark plugs, I then just let it run or take it for a test ride? If I just let it run, how will I know if I have found the culprit?
Do this test at idle on the centrestand. You don't need to remove the plugs. Just pull a plug cap off the plug and see if that alters the way the motor is running. It should be obvious if that cylinder stops firing. If nothing changes, however, it indicates that the cylinder is already failing to fire, so you know which one is giving you problems.
However, before doing any of this, remove each plug cap from the ignition lead and trim 1cm off the lead. Then screw the cap back into the lead. Reason for doing this is that over time, the core of the plug lead corrodes and fractures causing a poor contact and weak spark. With luck, this might be the reason for your misfire. You'll know soon enough ...
Good news my beloved FZS is back on track!
Thank you so much for your help, Mike! I really appreciate it.
I had first shortened the ignition lead but that didn’t fix it.
After that I did a couple of things, so it’s hard to say what it was.
What I did:
- I put contact spray on the ignition leads.
- I removed the spark plugs and tested them with a volt meter.
- Some of the spark plug gaps were slightly big so I adjusted the gaps.
- The rectifier plug seemed fine but I cleaned with contact spray and a brass brush.
So, I really don’t know what it was but happy, it’s running again!
Well done Julius for getting it sorted. Fingers crossed for many more trouble free miles.
[/size]Good to see you’re still loitering on these pages Mike, sharing your wealth of knowledge as ever. Hope you’re keeping well. ?[size=small]
21-08-23, 04:06 PM
(This post was last modified: 21-08-23, 04:43 PM by jul1us.)
Haha, it seems I rejoiced to soon.
So now, it was mostly running perfect but there was a slight bit of stuttering a couple of times which seems to indicate that I fixed it but not 100%.
Is it perhaps possible that the spark plug caps are somehow corroded or not 100% okay?
Also, in my case the plug don't screw off from the ignition lead but can just be pulled off.
The day it went bad was a really hot day and I was keeping the revs really high so I am thinking it was caused by heat?
Also, this is a picture of the rectifier plug:
https://i.imgur.com/He0hafK.jpg
Would it be visible if there were something wrong with it?
Edit: I just measured the resistance of the spark plug caps. All but the cap of cylinder 3 had around 9.6 kOhms, the cap of cylinder 3 had 11.6 kOhms. Could this be the reason?
Will take it for another test drive now...
21-08-23, 07:31 PM
(This post was last modified: 21-08-23, 07:59 PM by jul1us.)
So, I took it for a test drive. The first 15 to 20 minutes it was almost perfect, only three or four misfires in total, hardly noticeable.
After that it deteriorated rapidly and now I'm back to square one.
I'm now wondering if it's actually the spark plug cap or what else it could be.
Edit: This is what someone in the German forum wrote to my initial question:
"This sounds like voltage problems with the ignition system. The exup fault could be a side effect. An exup fault will not cause the engine to stop.
I would start by investigating if the 12V is coming clean to the ignition. A simple bulb on the 12V supply side of the ignition coils may give some initial clues.
Second important thing is the starter relay and all its little switches. This can also block the ignition. To rule that out you can temporarily replace the relay with wire jumpers.
What I have also seen are cracked plastic housings of the ignition coils. There the spark jumps directly to ground. But this can only be seen in total darkness."
21-08-23, 10:06 PM
(This post was last modified: 21-08-23, 10:08 PM by unfazed.)
Looking at this it sounds
1. like and Air leak on the intake
2. a plug cap or two gone high resistance
3. Fake NGK Spark plugs
For the air leak, check the Vacuum take off caps, the intake manifolds are seated correctly and the rubbers from the air filter are seated correctly
Thankfully the plug cap can be dismantled, they can corrode internally and the 10kohm resistor which is a carbon resistor can go high resistance. Unscrew the the plug holder in the cap and you should have the screw section the resistor and a spring. The Base the spring sits on inside the cap needs to be cleaned, I usually clean it with a long very thin sharpened screwdriver as this is the easiest option. The spring may also be corroded and needs cleaning with wire wool or something. Finally I replace the resistors with those from faulty NGK plug caps as these are wire wound and stainless ends. Thses are only 5kohm but it is not a proble as they are only to prevent interference Yes NGK plugs also suffer from internal tarnishing which can send the resistance in the high megohm range and screw up the spark. I have come across plenty of them, the latest was last Saturday on a 2002 Triumph Bonneville 800, broke it open in front of the owner to prove it. At least the NGK caps are a lot cheaper than OEM even if you need to break open a new one for the resistor. when finished cleanin off all the corrosion put them back together.
Fake NGK plugs can be difficult to detect but close inspection will show poor printing, engraving and sealing washers. Only way to avoid them is to buy from a reputable source. Very risky buying ones at knock down prices
21-08-23, 10:26 PM
(This post was last modified: 21-08-23, 10:46 PM by jul1us.)
Update: What I had completely forgotten: I have a lithium battery with charge indicator, and it was all the way down this morning, whereupon I charged the battery for half an hour (not longer, because I wanted to test then).
After that, the Fazer ran better for about 25 minutes and then got worse again (as described above).
Now I just went down and measured the battery with the bike turned off: 13.48 volts and when I start the engine it is only 13.51 volts. Does that mean the rectifier or the stator are gone and would that also explain the engine problems?
Tomorrow I will repeat the test and rev up the engine which I wasn't able to now because of my neighbors.
Thanks, unfazed! These are great tips! Do you think that 11.6 kohm is too much for a plug cap? (One is at 11.6, the rest at 9.6)
I don't think the spark plugs can be fake as I bought them over the counter at Germanys most reputable motorcycle dealer (Louis).
Don't you just love random faults? No, didn't think so ... 
With Unfazed on the case you're in the best hands but a few thoughts from me:
Plug caps shouldn't just pull off the lead. It should be a really secure, screwed-in connection. This sounds suspect to me.
Also, it sounds like you have a battery voltage drop issue - potentially not charging - which could explain why it ran fine for a short while after you boosted the battery, then started misfiring as the battery voltage dropped.
The contacts inside the rectifier plug look fine but have you inspected the cables where they enter the connector block? Look for signs of overheating or other damage.
You haven't mentioned if you checked the earth connections. Many intermittent electrical faults have their root in dodgy earths.
A useful thread on replacing the reg/rec connector block to eliminate that as a cause/future source of problems
http://www.fz1oa.com/eskortsdefectivecon...ment.shtml
Another thought occurred to me. I assume that your lithium battery has a good BMS inside to regulate the voltage going into the battery from your alternator.
I don't know much about lithium batteries on motorcycles but I am aware that they are voltage-sensitive and the charging output of older motorcycle systems isn't always compatible with them. Also, if you have any issues with low output from your alternator your battery may not be charging as it should:
https://fulbat.com/wp-content/uploads/20...um_PDF.pdf
Can I just jump in here & offer some info that you may or may not be aware of ...
Been reading this long winded thread with interest, good on ya for having a go at the carb mods, albeit you've had multiple issues along the way.
Lithium batteries need a proper full charge from a Lithium spec charger prior to use, or they can never fully function as intended, also most bikes Reg/Recs especially older bikes like our Fazers were never designed to run a lithium battery, this might be where all your gremlins lie.
For this reason, I would never use a Lithium on any of my bikes, plus they have been proven to cause fires.
Might be worth swapping out the Lithium for a fully charged lead acid battery & see if there's an improvement.
You've obviously got other gremlins to diagnose, but Mike as always has given you the heads up on what to check already.
22-08-23, 12:52 AM
(This post was last modified: 22-08-23, 01:21 AM by jul1us.)
Thanks, Mike!
I'm actually learning a lot and do enjoy a bit of tinkering so it's not all bad. I'm also improving my bike as I will definitely replace the rectifier plug. Anderson Powerplugs are already ordered.
I will take a video of removing my plug caps tomorrow.
How do I check the earth connections, is there a thread on this already?
Thanks, Gaz66!
I did fully charge my Lithium battery with a lithium capable charger before first time using it.
Schlumpf (the creator of the multigauge) actually recommends the usage of a lithium battery for the fazer as it starts the bike much easier (and weighs less). These lithium batteries have a built in controller which manages the 14V charging current.
Quote by Schlumpf: "I've been running a LiFePO battery for many years now. They seem to cope better with the tendency of low voltages of the Fazer."
His website is quite interesting, you can read it google translated here:
https://cvieth-bplaced-net.translate.goo...x_tr_hl=en
If you go on the drop down menus on left side to motorcycle -> FZS 1000 you can see the sub categories.
22-08-23, 01:32 AM
(This post was last modified: 22-08-23, 01:58 AM by jul1us.)
Thanks, Mike!
I'm actually learning a lot and do enjoy a bit of tinkering so it's not all bad. I'm also improving my bike as I will definitely replace the rectifier plug. Anderson Powerplugs are already ordered.
I will take a video of removing my plug caps tomorrow.
Is this how I check earth:
"Put the multimeter in your lowest Ohm setting and put the black probe on the negative battery terminal.
Then probe around on all the lights negative wires whilst giving them a wiggle. You should be getting very low readings."
____________________
Thanks, Gaz66!
I did fully charge my Lithium battery with a lithium capable charger before first time using it.
Schlumpf (the creator of the multigauge) actually recommends the usage of a lithium battery for the fazer as it starts the bike much easier (and weighs less). These lithium batteries have a built in controller which manages the 14V charging current.
Quote by Schlumpf: "I've been running a LiFePO battery for many years now. They seem to cope better with the tendency of low voltages of the Fazer."
His website is quite interesting, you can read it google translated here:
https://cvieth-bplaced-net.translate.goo...x_tr_hl=en
If you go on the drop down menus on left side to motorcycle -> FZS 1000 you can see the sub categories.
Here is his electrical optimisations page :
https://cvieth-bplaced-net.translate.goo...x_tr_hl=en
Good morning, Julius.
The links you posted for Christian's site are very helpful. I wish I'd had them while I still owned my Fazer and R1. If he's happy with fitting lithium to the Fazer, that's good enough for me.
If I still had the Fazer, I think I would follow his advice to improve the wiring for the headlights and the earth connections. You might find the latter useful if you have earthing problems on your bike.
I also found his observations on the ignition lock (we usually call it the ignition switch) good, too. It reminded me of a problem I had with my Fazer which was traced to the red connector block wiring, same as in the photos in this link
https://cvieth-bplaced-net.translate.goo...x_tr_tl=en
You can test the earth connectivity in the way you indicate but I tend to physically inspect earths as well. Remove the earth cable bolts, clean the contacts and refit. As Christian notes, there's only one earth point to the chassis through the starter motor. Make sure that is all good.
It's looking increasingly like your problem is voltage-related. Hope you find it soon!
Cheers
Good Afternoon, Mike!
I'm a little embarrassed because it's so simple, but I found the problem. I was about to implement Christians advise about checking the the currents going into ignition coil, when I noticed that the one connector was so loose that it was wiggling around completely free. After tightening it up, I took it for a long test drive and all was well again.
https://i.imgur.com/hGVxnLr.png
https://i.imgur.com/ELBTJJg.jpg
Thank you again, and also the others, so much your help. It is really appreciated and I'm happy I learned a lot.
If you're not driving the Fazer or the R1 anymore, are you driving something else?
In addition to Christians electrical page, there is a guide in the German forum:
"Power Tweak or Relay for Ignition Switch Relief" which I can post in another thread here later on...
Good find! That's a relief, no? As you said, a simple thing but often easy to miss when you're fault-finding. I'm very glad that it was a quick fix once you looked in the right area. Christian is an awesome source of knowledge and ideas.
I sold my Fazer back in 2020 and the R1 in early 2021, just before we moved back to the UK from Spain. Too much expense and hassle to ship them back, although the value of original 4XV R1s in totally standard condition - like mine was - has gone up considerably.
Currently no bike in the garage and it will probably stay that way. I guess riding in Spanish weather on empty roads spoiled me too much!
Cheers
Oh, yes, it was a big relief. The moment I found that lose connection I was hoping I struck gold but also fearing that it might not be it. Then when I did the test drive full relief set in.
Overall, this really happened at the best time as I had the time to take care of it and also learned a lot about the bike's electrics during this time.
Thanks again for all the great support you have been giving me since the beginning of this thread, it has been a real life saver!
As announced here, I just posted the translated guide for the "power tweak":
https://foc-u.co.uk/index.php?topic=27821.msg332584#new
Diagram suitable for the early models with the lights on/off on the right handle bar.
From 2003 on, the turning on of the lights is controlled by the Ignitor
Hi. I notice the top connection to number 2/3 coil is the white wire. On my bike the top wire is red and black and the lower is white. Can anyone confirm which is correct.
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