Fzs600 low rpm stutter/bog down.

[Gnasher]

Yes a little low which would answer why it's not idling properly and the pilot circuit is restricted.  Your symptoms are classic air/fuel issues of the pilot circuit, something isn't right somewhere, the mixture is either too rich restricted air flow or too lean restricted fuel or an air leak too lean.  you mentioned you've changed the intake rubbers are they seated correctly? Is the intake rubbers from the air box to the carbs correctly seated both sides and done up?  Is the air intake restricted, I've had bikes in where a rag placed under the seat has been sucked into the air box?

Have you seated the diaphragms correctly, when revved do all the vac needles move together or is one or more slower? 


Check the fuel level in each float bowl are they in spec? 

If after riding if you open the tank is there a rush of air?  If so try running the bike with the tank cap not click shut so it's slightly open, if it idles properly check the tank breather pipe, this is one of the 2 that are connected under the tank, the other is the fuel cap drain.   

Bypass the pump and run fuel straight from the tank see if it will idle and run below 5k, it it does it's the pump.

Give that lot a go see where you get.

Failing that it's got the be either a choke plunger not fully returning or the pilot circuit is restricted somewhere.