Trouble with bike

[Oddjob]

Yeah that's a Kokusan. Are there just 2 wires coming from it?

If so, try swapping them where they go into the harness near the engine mount. Try the engine and see if it's better or worse. If worse swap back.

The symptoms really sound like a coil problem BUT it could just be a coincidence, maybe it's a carb blockage and it just appears to be coil related. Let's get the coil out of the equation and move on from there.

[McCabe-Thiele (Ted)]

If you have the original points plate & advancer might be worth going back to points to for a trial period.
Although I have an (unbranded) electronic ignition unit for my 500 I am still on points at the moment.

To be able to run on 2 cylinders running/working  on separate coils,  seems unlikely (though not impossible) that both the coils are failing to produce the next required spark.

I don't know enough about how coils work to say that with any confidence. As each coil is producing a wasted spark I would expect a spark generation issue to affect all four cylinders.
I have the Hendler coils on my 500.

[beardylondon]

no I don't have original points, I bought it with the electronic ignition.it ran fine when I bought it 4 years ago and even better after I had the carbs cleaned and balanced 2.5 years ago.

[McCabe-Thiele (Ted)]

When you fitted the replacement coils what plug caps did you use?
Is there any possibility of a poor HT connection at the caps ?

[beardylondon]

Genuine NGK ones, I spent some time weeding out the fake ones and made sure they are genuine.

Further update:

On fully charged battery, the spark on all 4 got a little bit bluer, but the spark was quite small and dancing around.

Also, all 4 plugs look the same, so must be getting the same power etc?