I have 2 custom bikes. I am not unusually proportioned, so I can't argue that I "needed" a custom frame, but I had enough slight quibbles with what I saw in stock bikes that it seemed to me as if going the custom route made sense.

In the process you have described above, I think you have 3 things working in your favor:

1. Indy Fab makes good bikes. However, the fit of the bike will only be as good as the person doing the measuring and interviewing of you, which means that you have to trust...

2 ....your LBS. Sounds as if they are experienced, and you trust them.

3. Finally, once you and your LBS have invested this much time and $$ in the process of putting this bike together you'll both have plenty of motivation to work out any kinks in the initial delivery. Tweak the set-up, stem, saddle, or whatever, and you'll get to what you want. On both of my custom bikes, I was delighted right off the bat, but I kept tweaking until I was 100% done. With bike number 1, I ended up changing out the gearing, did lots of experimenting with stem height, changed the tire size, and finally arrived at a happy place. With bike number 2, I swapped out the handlebars after a few months, and then I was perfect. In both cases, the frame was great right off the bat, there were just minor tweaks after many miles of riding that made the bikes "perfect."