Hey Adam,
I ended up with an Independent Steel Deluxe. It has all the rack mountings and a 45 cm chain stay.
http://www.ifbikes.com/OurBikes/Off_Road/Steel_Deluxe/
Before you dispair, though, think about getting a Tubus Logo rear rack. It allows panniers to be mounted a bit to the rear. Talk to Wayne at the thetouringstore.com. Also, Arkel sells panniers that work best with short chain stay mountain bikes.
http://www.tubus.com/en/rear-carriers/logo-expedition
http://www.arkel-od.com/panniers/xm4...asp?fl=1&site=
The money you save in not buying a custom fram can be used to buy a rack and some new sweet panniers.