2000 FZS 600 runs lumpy after a trip to the Alps

[unfazed]

Hi guys


Been lurking as a guest for a while but as I'm about to take the bike to bits I thought I would ask some advice to make sure I'm on the right track:


Backstory:
English guy living in Belgium, passed my test about a year ago and bought a fabulous 2000 Fazer with 42000 km on the clock for what I thought was a great price. Rode it to the Ardennes, rode it to work, rode it every time I could, it started up great every time and had me smiling from ear to ear. A big group of us planned a longer trip to the Alps so I prepped the bike with new tyres and a small service (oil change and once over from a local guy).


[size=1em]On the trip everything was fine until about the third day when we were at the base of the Alps. I had been putting the cover on the bike at night but regrettably I didn't do it this time as it was such good weather when we went to bed, it chucked it down all night. Went to start the bike in the morning and it was not raring to go like normal. No low end power, revving the engine just to keep it going, petrol smell from the exhaust. I adjusted the idle screw so it would run and made my way, albeit cautiously, up the alps in the continuing rain and heavy traffic. It was horrible bunny hopping round the hairpins. After about 3pm it got warmer and sunnier, I started to notice she was running a bit better. After stopping for fuel I hit the start button and it sprang to life like I was used to! Self healing bike![/size]

[size=1em]On the trip back it rained again and all the old problems came back. What a bike though; it still got me home. [/size]It still has the same problems after sitting on the drive under cover for a few days, weather has been sunny with intermittent heavy showers. It will run if I turn it over for a good 10 seconds and give some gas but it doesn't want to keep running.

I suspect it is the coils as the exhaust for cylinders 1 and 4 get hot but 2 and 3 don't. I've been reading that 2 and 3 are on one coil whilst 1 and 4 are on the other. I also suspect the carbs need cleaning as petrol pours out of one of the overflow pipes when it is running. If the pilot jets are blocked this would explain the cold exhausts and bunny hopping at low revs. I have been reading pointer2null's post (http://foc-u.co.uk/index.php?topic=91.0) about carb balancing

Jobs:
Remove tank to get at it
Check coils: Can I just swap the HT leads from 1 to 2 and 3 to 4 to test them or will they not fire at the right time?
New spark plugs all round
Check compression
[size=1em]Adjust valve clearences[/size]
[size=1em]Remove carbs and give thorough clean[/size]
[size=1em]Balance carbs[/size]
[size=1em]Replace the rubbers: I originally thought this might be the problem as they are all cracked and split[/size]
[size=1em]...[/size]

[size=1em]Anything else I might have missed let me know[/size]

To be honest is sound like plug caps arcing due to water ingress.
First thing I would do is replace the plug caps with NGK ones and before you fit them cut 10mm of the wires.
In the mean time to get the bike running remove the 4 plug caps and spray WD40 into the top and bottom of them cut 10mm off the wires and put them back on.
Do not cut 10 mm off the wires twice.