You might want to look at Universal Cycles in Portland, Oregon http://www.universalcycles.com/wheelkit.php

Look at their custom wheel builder and dial in what you want. I believe the total price for a wheel set is less than the cost of the individual components. Their prices are competitive, their wheels are excellent, and their customer service is great. I have had 3 sets of wheels built by them, and they do do a high quality job. I just had a set of wheels built for one of my touring bikes. I used Shimano 105 hubs, Velocity Dyad 36 hole rims, and Wheelsmith double butted spokes, and the cost of the completed wheelset was $301. Last year they had their Ultegra hubs on sale, and I got the same wheel set only with Ultegra hubs for my wife's bike for $291. .