USA
Custom Guitars from memory. - both John Nash and Bill Crooke build their guitars from USACG parts - Nash in particular considers them to be about the best around.
Having said that, I have just about finished a Strat made almost totally from Warmoth parts (solid Indian
Rosewood neck was why I didn't simply buy a Fender), and I have to say the quality is pretty high - the Strat body contouring is very deep and comfortable, and the neck is a cracker! It's worth remembering that Warmoth make and sell raw necks - they do good fret jobs, but they don't level the frets - they also don't roll the edges of the fingerboard - all that sort of stuff is in the hands of the guy actually building the instrument.
As far as cost on the Fender, I'd guess at more like $3500 - $4000 - I'm assuming that if you custom order a guitar from Fender, you're going to get hit with a MSRP, rather than a street price.