Coil or pick up coil

1980 Kawasaki 750. The bike was running the best it has ever run since a complete rebuild and a frustrating process of re jetting. Then when trying to start it again it will only run on cylinders 2 and 3. The timing advancer is clean and moves properly. The pick up coil assembly is new this year. The Accel coil a few years old. I have a good idea it has to be one or the other as it coincides with the pistons that are firing. All connections are clean with no signs of a short. How does one test to find the fault?   
 

For four cylunder/2 coil ignition systems.

Take all the plugs out. See which spark plugs & Note which spark.
Swop the coil trigger feed wires around. 
Check which plugs spark. 
If the spark swops onto the other pair of plugs then it's the pick up coil. 
If it doesn't then it's the ignition coil. 

You can also double check the pick-up coils by connecting an LED test light across the two coil terminals (the LED should pulse with engine rotation)
PS: don't forget there is an igniter between the picks and the coil unless you are running a "Dyna" system so no pulse doesn't automatically mean the pick up is faulty