TB,
Just read through the entire thread. Looks like you are getting pretty serious. I am going through this process except with a Gunnar Sport.

Just wanted to add some comments.

Having built up two bikes now I can say that there is almost no way that a new build-up can compete pricewise with a the price of a new complete build. An alternative can be to buy the complete if it is close to what you want and then change out the remaining components and sell them back to the LBS for credit. Or, of course, use parts you already own.

When buying on flea-Bay I have come to take into account an extra "cost enhancement factor" due to mishaps that happen during the transactions. These mishaps range from outright fraud to counterfeit or defective parts.

On my latest build I am working through an LBS and buying everything from him. I went through what you are doing in terms of shopping around on the internet to put together the initial estimate. I didn't tell him what that was. Fact is, his estimate is coming in below the lowest of what I can do mixing and matching from Jenson, Nashbar, flea Bay etc. On average I am paying 78% retail for the components (installed). There is less of a discount (85%) on the frame. Plus, he will warrantee and adjust the bicycle which is important since it is not a standard build and in my experience there are always early problems to sort out.

Good luck.