Parts 2 and 3 of this series seem to be in limbo until I figure out what the issues are. However I have now solved another issue.
With the server PC, I have on-board graphics and an AGP slot with a graphics card in. This AGP card was enabled for the install. I found that the system would not boot if the monitor was connected to the AGP card output. After some research, I found that you need to connect the monitor to the on-board graphics out (or at least this is a fix to a similar question on the issue).
So I re-connected the monitor and entered the BIOS and set the primary graphics to PCI (on-board) and then tried again. A bit of cable swapping later and I can now or should be able to boot the server without the monitor being connected. Importantly I can also login via ssh and shut down the system again fully headless.