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?