I'd focus on the alternator wires (3 yellow, one white and one green). The oil pressure and neutral switches are on the ground side of the system, so if either one was shorting out the indicator lights would come on/flicker. The heavy cable for the starter only has current going through it when the solenoid is closed. If the sparking only happens when using the electric starter, it could be in the starter motor cable.
It won't hurt to look them all over, but the alternator wires have current in them as long as the key switch is on, so I'd start there. Sometimes the wires can get pinched in there.
Try an impact driver or screw extractor on the sprocket cover screws first. The cover has to slide towards the back of the bike a bit before it can be removed, so drilling the heads off won't really allow for removal. You could also try Dremeling a slot in the screw heads and getting them out that way...