I had a situation where # 2 and 4 were not firing. It was extremely strange, when the plug was gounded agains the case, there was no spark, but as you pulled it away, massive blue arc across the electrode, and to the case.
The problem turned out to be that I had used resistor plugs (dr8esl, what the canadian bikes use) and resistor caps ( what the american bikes use, in conjuction with non- resistor plugs) I put d8eas in, and she purred like a dream.
Have you already tried checking the resistance on the caps and plugs? one or the other of each should have a resistance of 5,000 ohms. If your spark plug caps haven't been replaced, you may want to do that anyway, it's a relatively inexpensive insurance plan, if you will.
Hope this helps!