I think if you want a seriosuly killer strat, you could have it put together by a good tech using parts from Warmoth and stewmac and come up with something as good or better than any high-end strat, for a better price.  
The quality and availability of aftermarket parts has never been better.  I had the opportunity to try out one of the new Gotoh/Wilkinson "vintage" trems the other day (a 6-screw instead of a 2-post, but funky looking like a Wilkinson) and it's miles better than the old standard.  Likewise, nuts have advanced incredibly over the past few years, locking tuners are better and cheaper than ever, and some of the finished bodies coming out of Warmoth are stunning.  You can get killer pickups from Lawrence (or Duncan/Dimarzio if you're so inclined) and there are lots of people out on the web (like Custom Rewind) who will custom-wind pickups for your individual needs.  
It's definitely easier and cheaper than ever to get a truly custom, unique guitar, well below "Custom Shop" prices.