No2 cylinder not running

Hi
i have a 1978 KZ650 imported from the USA,(I am in U.K.), just changed the ignition system to a Dynatek DS2-2 complete with coils and leads, new plugs, set up as instructed and started ok but no 2 cylinder isn’t running as it should, the header pipe doesn’t get anywhere near as hot as the other 3, I have only run it on a remote fuel tank so the vacuum pipe which is attached by the no2 carb is not connected, could it be a fuel problem just on no2 carburettor? , timed with a strobe and all looks good.
thanks 

You have caused your own problem and then answered your own question.
The vac pipe on number 2 isn't connected so will be favouring drawing air rather than fuel which will cause that cylinder not to run correctly.
You must NOT run the engine without the vac line connected to a fuel tap or temporarily capped off.
 

As Zed1015 said, when using an auxiliary fuel tank, the vacuum line that goes to the petcock must be plugged. If the line has been removed from the carburetor, then the port on the carburetor must be plugged.