ok, so depending on how you look at this it's either good news or bad news...
I renamed xorg.conf so I could carry on configuring the device, but out of sheer curiosity I unplugged the HDMI rebooted and tried to connect via VNC and it worked.
I think I potentially know why though, and digging back into the memory banks I seemed to remember from using tightvnc to support racked servers that it launched its own desktop rather than the one seen at the vga port on the kvm in the server room.
From what I read here it seems that the xorg.conf is only needed if using x11vnc as it expects to ride on an open desktop, whereas tigervnc (or indeed any vnc server) will launch its own desktop:
Anyhow, all sorted, so now all I need to do is connect it to the scope, learn all of the necessary software, connect it to the relays controlling my roll-off roof,make a weather station to close the roof if it rains as its a remote-ish obsy, learn how to focus the scope and learn about astronomy.
So that's the next 10 years sorted...
Thanks for helping to wake my brain up Wolter, people like you are helping me keep sane in these very odd times.