Part of the potential for saving money is to treat the build as a project. Get your lists of parts in order including alternates. Have solid price estimates attached along with where those prices are from and then shop like crazy, buying parts when and where they come in under your estimates.
For example, you may have the best price on parts from XYZ but in another month or so, XYZ will have its traditional spring sale. As long as XYZ doesn't raise the price of your parts for the weekend of the sale then you will do well to wait. (There are shops in this business that do just that to improve their performance).
Option 2 is to price the same parts as take-offs (from a bike breaker who parts out complete bikes) from some of the more reputable Ebay houses. (Or Jenson USA who are very good for take-offs).
Option 3 is to price last years parts instead of this years although I suspect that you have already done this with the X.9 stuff based on your price. I am presently awaiting my brand new PG980 cassette from Cambria at """"34.95"""""

because it is a new 2006 piece. In this case I have been looking at several high end SRAM cassettes for quite a while on Ebay and through several IBS's. When I saw this price I knew how much lower it was that all other options.
Once the box is full then you can negotiate with the LBS for the build.
What I ment to say in the earlier post is why don't "you" try the build yourself. If you have a problem or a difficult piece of the puzzel to do, the LBS will still be there to perform that task. This looks like one of those once in a lifetime (yea right I know the N+1 rule) builds and you can make it completely yours.