Gunnar frames offer a pretty inexpensive way to get custom geometry. Base frame is $950 (Gunnar Sport), custom geometry is $1300. You'll need to add a fork to that, but the whole thing comes out to be pretty reasonable for custom. I have one, like it - mine is a Gunnar Crosshairs. I have an issue with a neck injury, a long torso, long legs and comparatively short arms. Going to a custom frame really helped make a comfortable bike for me.
My main bike is an
Anderson from Dave Anderson in St. Paul. Just a gorgeous bike to ride - but not cheap. That said, it's got the perfect vertical compliance I want, the perfect fit, perfect handling, etc... Comes in at around 16.5lbs for a 56cm frame.
I've also been looking at the
Habanero cycles for a disc based frame as well. Really been impressed with the conversations I had with them.
Another choice that could be really good is
Rodriguez Cycles on the west coast (Seattle or portland, don't remember which). I really like their approach to frames and they tend to priced pretty well too (inexpensive).
I'd be very ok going with any of these. Yes, you can probably get a standard frame to fit. But if you have the cash and you want exactly the right thing for you, then I'd not be scared of custom at all. It's worked out really well for me.
In general, it's important to get a frame builder who is going to listen to what you have to say. And it's just as important to make sure you can verbalize what you want. It's important to quantify the performance you want as best you can and then get them to tell you how they are going to implement that. Communication is key. The reward is you can get a bike that really fits your application and body well.
J.