Well, after what seems like an eternity (well, it is 4am and I've been at this for about 3 days), I've finally got the serial port working reliably at all speeds with my emulator. It's a bit annoying that I've spent so much time over a serial port, but I've learned a lot about VHDL in the process and realised that I've still got a lot more learning to do before I'm even half way competent.
I'll post links to some really useful VHDL resource tomorrow when I'm more awake! (I have actually already been to bed once already tonight, but I kept waking up with ideas...)
Anyway, the real point was that if I can't get a serial port working, what hope have I of getting a high-speed SPI connection working (especially without a useful debug system in place!) So, that's conquered now.
So, tomorrow, tomorrow... I need to get something good done before New Year. I can't decide between CRTC emulation or getting the SPI working on the flash chip or a serial based bootloader so I don't need to rely on rebuild the FPGA image completely just to change a few bytes of boot code.