Uninformed opinion here, but I want to respond anyway.
Most of the boutique builders are using the same tube sets on their high end frames as the big companies. I would have thought that the biggest quality difference is going to come in the attention to detail in setting up the frame and the accessories hanging off it.
There's going to be precious little difference on things like wheels and forks, as even the best custom frame builder will usually grab something off the shelf (unless they're making a steel frame). If you looking at carbon or alloy/carbon, I think it's going to be after-sales and aesthetic differences that are going to be most noticeable i.e. a good LBS with a mass manufactured bike may get to sitting/fitting just as well as an artisan who custom builds you a frame.
Then again, I just bought my first new bike (Orbea alloy/carbon) after riding for years on steel framed second hand stuff, so I'm not exactly sure what dropping $20,000 on a bicycle really gets you anyway, other than pose value (which can be worth a lot, but not to an weekend grinder/weekday commuter like me).
Personally, if I was racing, I'd grab something durable with a good warranty, and find someone (artisan or otherwise) who would build a bike to my exact spec including bars, wheels, fork, seat, seatpost etc. Big manufacturers make cost cutting a fine art and isn't always obvious (headsets, bottom brackets, cables etc). You probably don't have the resources of a pro team who can deal with mass produced frame issues and don't mind going through lots of bikes in a season. It may pay in the long run to find a good framebuilder and stick with him, even if it is only because they can be hassled more easily to fix broken things and you get more control over the components when the bike is built up.
cheers,
dave.