If the bridge and middle pickups sound fine in the # 2 position, it sounds like the neck pickup is wound in the opposite direction compared to the bridge and middle pickup. Normal vintage style Stratocaster pickups are wound top left (TL) and wound top going (TG). It seems that the neck pickup may be wound top left and wound top coming (TC). This would cause the coils to be electrically out of phase and you would need to reverse the winding direction or remagnetize the neck pickup to North polarity. Not many repair shops have magnetizers to work on pickups and you should send the pickup to a qualified pickup repair shop to do the work. Contact some pickup builders and winders advertised in Vintage Guitar Magazine and make sure they can do the necessary work on the pickup. I would have the pickup re-magnetized instead of rewinding for two reasons. It keeps the coil original and it is less expensive to re-magnetize than rewinding.