Interesting about the Stan's wheels, I dropped into the LBS again today. They say that these aren't custom built; they just get them shipped in and have their guy check for even spoke tension, that's about it. That was how they responded to my request for suggestions for affordable touring wheels. They do specialise in touring and most of the staff are cycle tourists themselves (i.e. not the typical teenagers who don't know what they're selling unless it's made of carbon fibre), so I do respect their opinion on this.
However, they are also perfectly happy to do true custom wheels - I know they used to run wheelbuilding classes, so I assume someone in there knows how to do it - but they said that they aren't cost effective unless I'm unsupported in the third world, crossing the Nullabor or something like that.
As it happens I do want to cross the Nullabor unsupported. If your wheel busts out there, there are a few sections where you'd be pretty much screwed.
What about building my own wheels? I am mechanically minded and generally enjoy this sort of thing. I have access to a decent truing stand - though I don't have a tension meter.