I have stripped the carbs 3 times and checked the coil leads and I still have a slight misfire, which I have narrowed down to cyl 1, my next task I think is have the rocker cover off and check the valve clearences, I would do a compression test but I don't have a 10mm adaptor.
The misfire or splutter is just over tickover, and it is till 2k revs, I have had the carbs apart 3 times, I have just ivanised the carbs which has made no difference. The misfire I mentioned was the spark plug wells full of water, I have fitted new plugs because of water in the plug holes, and the plugs starting to corrode, I know the plugs were not at fault, I did have an issue with no2 spark plug cap not sitting right but that is now slitting properly.
The standard Yamaha plug caps are not the best quality in my experience. I noticed this by accident on my mates fazer 600, fired the bike up in his garage when it was completely dark and noticed all 4 caps were showing visible sparks on the outside of the caps. They were arcing all over the place, spoke to a friend who is a Yamaha technician who said he changed all of his own bike caps for jet ski ones. I have done this on both my Fazer 1000 and my R1 and noticed a smoother idle especially on the Fazer.
Jim.
Sounds like a piece of metal in the pilot system from the Ivanising modification.
If misfire/splutter is one cylinder then it is most likely carb related.
Swap the coils and plug cas and see it it changes. If it does its plug caps if not its the pilot circuit.
When you had the carbs off did you remove the pilot screws and blow out the orifices?
Somebody on the forum had this problem and posted it some time ago
Well my low end misfire/splutter is now history, one or the leads had corrosion on the internal copper strands and when I screwed the cap back on the pin inside the cap sheared probably because of the corrosion.