With all due respect. The expert you should be asking is Robin Thorn, His shop has built hundreds of frames and he has a good idea of what works on his bikes. I seriously doubt he nor any other established builder will allow you to dictate the angles and chainstay lengths. If you want to go down that road that are plenty of starving wannabe framebuilders on the west coast that will burn together any concoction you want.
Chainstay length is just one part of the whole design. I have a similar bike to the Thorn, I have 49cm chainstays but I also ride a tall (63cm)frame, wear size 13 shoes and climb sitting down. If I rode a small frame (54cm) and my climbing style was "stand and stomp" I would want chain stays probably around 44-45 cm.
Head tube angle is just one part of how a bike handles, you also need to know what the fork offset is and how that will affect steering trail (caster effect). On a rigid fork those three parameters also dictate the amount of flex in the front fork. If you want to use a suspension fork you would then have have to consider the fork offset first since most suspension forks come with no choice of offset. Then you have decide what the steering trail will be and adjust the steering tube angle accordingly.
http://www.kreuzotter.de/english/elenk.htm
Sounds like you want a bike to do two diffrent things. What often happens is you end up with a bike that does neither well.
