Z650B1 Cylinder 3 Fuel Feed Problem

Hopefully someone can come up with some ideas to help me !

The symptoms are that the bike starts fine, but fluffs and dies when I open the throttle. #3 pipe stays cold, while all the others stay hot. When I put in a Colortune plug and looked, I could see a healthy spark, but no blue/yellow to indicate fuel is getting through.

I'm pretty sure it's a fuel feed problem, but I've checked/tested so many things my brain is turning to jelly and I've run out of ideas !

To rule out ignition issues; the coils, leads, electronic ignition and plugs are all relatively new, but I'd have expected an ignition issue to show up on both #2 and #3.
There's a separate issue where the bolt is seized onto the right hand end of the crankshaft so I can't directly get at the timing weights, but I can get a thin screwdriver in there and they aren't stuck.
Valve clearances are checked and good.
There is good compression (and more importantly, it's very close on all 4 cylinders !)

Here is the weird thing.... I've got 2 sets of carbs, both of which I've had apart and cleaned (repeatedly - the fuel around here is high in ethanol which has caused all kinds of issues, hopefully now solved with fuel stabilisers etc). And with both sets of carbs, the problem is #3 cylinder.

I've put a brand new manifold rubber, clamp and vacuum plug on, and can't find any sign of a vacuum leak, even though this was my first suspicion and this is what the fault seems to mimic. I've tried running #3 with the air filter pod off (I've used the kind of decent quality pod that doesn't block the air intake passages for years !), and tried adjusting the air screw to see if that makes any kind of difference - they are the version of the VM24SS with an air screw at the back not the pilot screw underneath.

What am I missing ?

Make sure the pilot jets are open by holding them up to a light.  And shoot carb spray through the pilot passage, watching where it comes out in the carb throat.  All carbs should be the same.  And needless to say, all O-rings must be fresh, and properly sealing.

Yep, I've done that, and just done it on the spare set ready to fit them tomorrow and try again. I've had endless problems with the ethanol fuel eating older o-rings, so I replaced them all with viton ones when I rebuilt the carbs, and they all seem to be good for now. I'm a bit of a compulsive o-ring-replacer 

Since this happens with 2 different sets of carbs, it makes me think it is not carb related. I might suggest you try moving the current #3 spark plug lead/cap to #2 and use the current  #2 lead on #3 and see if the issue follows it #2 or not.

Is no 3 plug dry or wet after trying to start it? Colourtune is effectively changing the spark plug so if it sparks on colourtune it should spark the plug. Does the plug spark when rested on the head? Where did you get the spark plugs, are they genuine or ebay fakes. Even genuine plugs dont last forever. Swop plugs 3 & 4 four and see if the issue moves with the plug. 
where in the uk are you. If your anywhere near brands hatch i can help.

Is the float bowl vent clear (no air in means no fuel out)

Unrelated to single cylinder misfire, but what changes did you make to the jetting to compensate for the pods?

Wow - thanks for all the replies ! I finished work at lunchtime and starting working through.

I'm an idiot.

After much checking, it turns out I was right about it being a fuel issue. Somehow between the last float height check and the most recent carb rebuild, I put the float for #3 in upside down. D'oh ! I'll check the spare set, in case I've replicated the error there.....

To answer your question about jetting for the pods, I've gone from 15 to 17.5 on the pilots and 102.5 to 105 for the mains, and it previously ran happily like that - I've had it on K&N or S&B pods since about 1982 !

But something has changed, because it now runs on all 4 cylinders happily at tickover, but still fluffs, stumbles and dies when I open the throttle. To me, that still says I'm starving it of fuel, just evenly across the cylinders. I'm thinking first thing will be to re-check the float heights, then adjust the air screws (currently at one and a quarter turns out, as per the manual) to see if I need to increase the richness. I'm happy the pilots are clear and evenly matching carb cleaner squirts show the pilot circuit passages are clear. Getting this bike set up right after it spent time laid up has been a challenge !

Modern fuels are nothing like the old proper petrol and need the carbs set to compensate.
when its fluffing lift the choke slightly, if its better it needs more fuel, if its worse it needs less.
For pods you generally leave the pilots stock, go up one size on mains and then fit air corrector jets to sort the flat spot at about 3k rpm.

Sorry for the delay updating.... work does this to me sometimes ! After a few days of craziness I was able to get an afternoon to carry on working on the bike.

It's still running on 4 cylinders, which is good, but it's not rideable. I found that screwing the air screws in from the standard 1 and a 1/4 turns down to 3/4 of a turn made the fluff at around 2K revs better. But at that point, there's a hint of white smoke from the exhaust that smells of unburnt petrol rather than oil. More worryingly, if I put it in gear, the bike stalls as soon as there's any real load on the engine.

I'm coming to the conclusion I need to educate myself a lot more, then go back to complete basics and try to diagnose every aspect from scratch rather than just assume it's the carbs. I wonder if it is possible that there are multiple problems that the tests I've done so far haven't isolated.

Am I right to wonder if the timing springs maybe are too weak (I can see it moves, so the timing adjuster isn't stuck) ? But due to the bolt that has been seized onto the right hand end of the crankshaft for the best part of 35 years, that's going to be very tough to get to, check and (if necessary) fix.

Or is there something else I should check first ? Compression and valve clearances are both recently checked and good, and the ignition system is also mostly recently replaced and checked - the only part I couldn't replace was the plate (that damn bolt again....), but it all tested good.

It almost feels like I should fully refurbish one of the bad engines I've got (two, both with knackered heads), put that in and see if it still misbehaves !

Over fuelling is normally black smoke- white or grey is normally oil !!!

Ah - thanks for that ! I've got a lot to learn 

In that case, I'll keep going richer. It wasn't the kind of plume I'd expect from rings gone, just a slight whiff of it, so could have just been that the engine wasn't warmed up yet, or perhaps condensation inside the exhaust getting blown out.