Serotta, Indy Fad, Moots, Seven, Dean and Merlin all come to mind as us builders but there are quite a few others. These makers all target the high end custom (usually roadie but also make mountain bikes) market. However if you were to go to them and tell them what you wanted i have no doubt they would be able to build you just that. Also just remembered there is a smaller company called Habanero that does custom titanium frames, they are still not cheap but are more affordale than most other makers.
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Road: Quattro Assi Scandium w/ SRAM Rival and Rolf Echelon's
Mountain: 2005 Specialized Enduro Comp
2003 Gary Fisher Tassajara