What do you mean by going back to standard? Are you back on the stock coils? So you have it narrowed down to the wiring or the MS box itself. Can you switch over to the stock ECU to control ign just to test your grounds and wiring?

 

yes i am using the stock coils, i have it on there with bullet connectors at the moment.
i cant use the stock ecu because i have the throttle bodies on there now.
i am going to try the capacitors on there before i change anything else,
the misfire has only happened since i changed the std coils for the motorbike ones.
now i have the std ones back on there the misfire has not gone away, i can only think its the wiring but i have shielded it (grounded a wire and wrapped it round the other wires individually)
is it deffo tach noise that causing the misfire???

 

you can add a 4.7nf caps in line with the tach input signal, and like Matt said, run tach input through shielded wire, that should reduce, even eliminate the spike.

 

thanks guys, you have been loads of help.

 

I'm almost certain. You are getting some sort of false triggering from the CAS for sure. Such false triggering can cause the spark to fire at the wrong time, or otherwise monkey with your ignition output. Garbage in, garbage out.