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.
As I had planned, I am still intending to use a CompactFlash card in IDE mode as a mass storage medium and boot the operating system from that using a minimal "ROM" to store just the BIOS and boot-loader for the system. As such, the IDE controller is going to have to be a feature of the mother board, as is the BIOS ROM, I have yet to decide how to include RAM in the system.
I have also decided that to allow a smooth upgrade path of my system to the Z80180 processor which has a 20 bit address architecture and to allow access to more memory the whole system will be designed around a 20 bit address bus and 8 bit data bus. Since the Z80 cannot drive all 20 lines of the address bus, I have pulled them low on the processor board via suitably large pull-down resistors, making it a trivial exercise to later add a memory paging module to the I/O bus to expand memory accessible to the full 1MB that 20 bit allows.
One thing I have discovered is that picking my logic chips carefully is essential. It would seem that TTL is not going to be practical for what I want, and pure CMOS isn't either, so I'm currently using all HC or HCT logic families to keep the design simple.
I also hit problems with my oscillator design, I found it very hard to get the oscillator to start off. In the end I've settled for a 4MHz ceramic resonator instead of a quartz crystal. This isn't as accurate as a crystal oscillator, but as I wasn't planning on making this system do any time critical functions (other than telling the time, but that will be done with a dedicated real time clock chip) this shouldn't cause a problem.