One of the hardest things about any electronics design project is capturing requirements. That's why after some careful consideration I have taken Mathieu Stephan's recommendation to take a look at the Easy-Phi project to heart. 

The Easy-Phi project is a very well thought out modular system that is compatible with the size and interface constraints I had already set for this project. Easy-Phi defines a backplane connector that will supply USB 2.0 connectivity as well as ample power and a reference timing signal. This, in addition to the eurocard form-factor I had already chosen makes this a really good fit and eliminates a lot of decisions I still needed to make about how I was to connect to the board. 

One issue I'm facing is that the template is in KiCAD and I plan to use Altium Designer at least for the initial layout, although I am very interested in re-creating my Designer work in KiCAD and learning what looks like a really strong truly Open EDA tool.

Mathieu's very nice introduction to the Easy-Phi template finally convinced me. You can read it on his blog here: http://www.limpkin.fr/index.php?post/2013/10/09/Easy-phi-project%3A-the-template-module

Arduino IDE compatibility FTW!