For a custom builder I would point you to James LeClair from Tampa. The guy uses really top notch woods, hand sculpts everything, does all the fretwork and inlays himself, and even hand winds all his own pickups and individualizes them for each guitar/bass. I guess the only thing he doesn't do is machine his own hardware. If you want contact info let me know. He's a bit hard to find these days.
Reverend Buckshot> Barber Tone Press> T1M Pearl> T1M AC/EC
Martin GPCPA3> T1M AC/EC
> TU-2> POG2> ib Mod NOVA delay> Sonic Stomp> Trinity Reverb