You've come to teh [sic] right place.
Best of all, it is not difficult to build a good Strat that will help you hook up with better looking women (check out the "Crushes" thread in The Dressing Room). Even I can do it, so anyone can.
Firstest, get it through your head: Fender and Gibson are factories. So are their custom shops. Not only that, Gibson and Fender were always factories, even back in the good old days. So forget about "black arts" or old-world trained craftsmen carefully tap-tuning Strat bodies and testing different pickup combinations on each individual guitar.
They don't do that at Fender, at least not for the standard mass-produced Custom Shop offering.
That is what you are going to do.If there is a magic, it is in finding the right combination of parts that work with that guitar. Sometimes it takes some experimentation. Sometimes you think you will get one sound, and you get another.
You can start with a good-sounding Mexican Strat and install some BKPs and better electronics and that will get you 90% of the way to a perfect Strat, unless you are a vintage freak like me. Then you can get some wood and parts and start building.
www.musikraft.com is a good source for fairly correct bodies and necks. Plus you can do something more interesting than improve on the standard Fender offerings.
The terminal stages come when you start chasing down vintage parts, staring at photos, and sniping Ebay auctions for a more accurate product.
I've already built several variations on my visions of perfect Stratocasters, and last times I took any of mine to music shops selling CS Strats, the sale staff agreed that my guitars killed the official Fender product. (I actually wasn't so certain, but everyone else was, and I was not fishing for compliments.)