wee nor

My bike is now fully rebuilt and ready to go. I balanced the carbs a little while back and it was running sweet with SP Engineering carbon cans fitted. Starting after paint job etc, it's running like a bag of ****, lumpy, popping back while sitting on the stand. First thing I thought was dirty carbs. Stripped and cleaned, no better. Fitted temporary fuel supply to rule out tank/filter. Again went back to carbs, set fully rich, no better. I rode the bike for a couple of miles and it ran on one cylinder. Pulled the plugs and the rear plug was washed clean. pulled the leads clear, I checked the plugs for spark, healthy ! pulled off the plugs from the leads, switched on ignition and heard a cracking/shorting sound. I checked the rear coil and it was shorting all over the place, unplugged coil. Tried again and the front coil did the same ! Is this a common problem ? Thanks.