I've been back home for just under a week now and I've actually begun construction of the system. I've made some important design decisions and discovered some useful facts for the continued design of the system.
The most important decision I've made is that the physical construction of the system should be very modular. I've started with the idea that the system is going to have a processor daughter card, a mother board, and a number of other cards that provide additional memory/interfaces etc.