wait for it dark then spray some water over the ht leads and cap and see if you can see very small sparks if you do then you need to change them hopefully it will be the caps if not new or second hand set off coils
Thanks for the tip, I will check this tonight.As above, new spark plugs and/or caps will likely sort that. Cylinders 3 & 4 are usually exposed to the elements if your bike spends anytime outside on the side stand. Spark plugs corrode, and a build up of dirt, water and corrosion around them doesn't help.
The bike has been kept inside for the last year, the year before it was outside but on the centre stand and usually with a rain cover. But it probably had it's share of exposure to the elements since the #3 spark plug was stuck in the cylinder head. Several months of soaking it in WD40 and working it back and forth did the trick. When the carbs were put back in for the second time new plugs were fitted. I'm definitely going to check the caps and the leads!
Firstly you've not mentioned the air filter at all, when was it last changed and what type/brand do you have?
If the bike can't breathe properly then it will affect the idle and lower revs, but can also hold you back at higher revs if it's particularly dirty.
Have you even looked into the airbox, it could be clogged up with emulsified oil as well, which my bike has had before.
As mentioned are the HT leads and caps okay?
You can trim the ends off the HT leads by 5-10mm, and maybe try new plug caps. Don't bother with new OEM ones as the price will make you fall over, but a lot of us have replaced them with NGK ones which work fine and are a great price.
http://www.ebay.co.uk/sch/i.html?_from=R40&_trksid=p2050601.m570.l1313.TR0.TRC0.H0.TRS0&_nkw=SD05F+&_sacat=0
A carb balance by the way will only work well when everything else is running properly.
So if your air filter is clogged (or you have an air leak), your TPS is breaking down or knackered, or your spark plug caps are on their way out then a carb balance will be irrelevant and can even make things worse.
Even the TPS positioned wrongly can make the bike feel a tad jerky at lower revs, i would do a check on that too, i'm on my 4th one now although this time i bought a brand new one at a much lower price than over here from Germany as it was all getting a bit silly buying used ones that were at least 13 years old and likely to peg out at any time.
http://www.ebay.co.uk/itm/Drosselklappensensor-TPS-101-Yamaha-FZS-600-DROSSELKLAPPE-13550-13D60-4HD-85885-/361403667980?hash=item542556560c:g:svIAAOSw2s1UxgsX
I did check the air filter, it was a bit dirty, not too much though and I managed to shake and brush away most of the dirt out, I put it back in because I didn't have a new one at the time. The box is clean but the small breather filter had some gunk in it which I cleaned out. Rubber inlets are intact. I'm gonna get a new air filter just in case, should I get the OEM one like the one I have or should I go the K&N route? Or is the high flow of the K&N going to screw everything up more?
Thanks so much for the link to the plug caps, they are at a great price! I did notice though that they don't have the 45 degree (more or less) elbow but I guess you didn't have issues with that since it has been done many times.
I checked the position of the TPS with the speedometer, it showed a tad over 5000 RPM so I twisted it back on forth and made it land on 5000 but theres a lot of leeway on both sides before the RPM needle drops up or down. How can you tell if the sensor is failing? You mentioned that you're on the 4th now, did you measure the resistance in the faulty one when replacing it with a new one?
Last but maybe fundamentally not least, the last fuel level measurement showed that carb #3 & #4 have about 1mm higher fuel level, could this tiny difference cause all this uneven running? Like I mentioned initially, cylinder #3 & #4 are running cooler that the rest, what's the logic here, is it because they don't get enough fuel or is it because they are getting too much fuel? Gonna check the spark plugs for colour later to get some indication.
Thanks for all the replies!