I have a Fender Custom Shop Relic Strat circa 1998 vintage. I removed the original single coil pickups some years back and replaced them with some afer market PU's, and now have decided to go back to the original PU's. The problem is, I don't know which pickup is which (neck, middle, bridge?). Is there a way to tell which is which, or does it really matter? I noticed that one PU had a red dot stuck onto one of the magnets on the underside. Does this mean anything?? Any advise / wisdom that anyone could share with me on this subject would be greatly appreciated.

The dot means bridge pickup or reverse wound. Get a multimeter, check the resistance of each pickup, and put the one with the most resistance in the bridge and the dot in the middle. You can also check the polarity of the magnets. If you can stack them all on top of one another, you have not a reverse polarity pickup in the bunch. That means the dot is most likely the bridge pickup.