78,
First you need to know what wire is the ground in YOUR wire harness. " Simple way without extra tools" You will need 1. a test light ($5 @ Auotzone, one length of wire; , and a test battery (the one that was in your motorbike). Take one wire and run it from the ground side of the battery to the frame of your bike ... secure. Now take the alligator clip on the test light and hook it to the + side of the battery. By touching the ends of the two wires you are running to the coil the one that lights up is the one that goes to the - (ground) side of the coil and is the ground to the coil. Doing it this way will make sure you have a solid ground and will avoid any other thing within the harness. Solid black or brown is usually the ground but not always. The second wire will be one color for one of the coils and another color for the other coil. I would then make sure that the other side of the coils are getting power when the switch is on.
By the way it was suggested that you swap coil leads and see if that changes which cylinders are not firing. did you ? This will at least tell you if it is the coils and not a wiring problem. RULE always make sure your grounds are good, then that you have power and after that everything else. Half the time it's a bad ground...'cause old motorbikes are,,,,,,,,,,,,,,,, well old motorbikes.
Cheers