Firstly, let me say, thanks for the help so far. You are a star. On Xmas and Boxing Day. Thank you. I know I'm a bit obsessive, but don't expect it from others, so know that ti was appreciated.
So I decided to do a new build based on what I have learnt to date, and I realised during that process that I had made an error in where I got the core files from. I am not a muppet often, but this was good example. I incorrectly used the files from the Probe_Basic directory. So I did a rebuild using the correct files from the Machine_setup_files.
And guess what??? It worked.

So forgetting the chair-keyboard interface issue, the instructions are solid with some caveats.
So here is some feedback from me on the setup instructions to help with the documentation for the muppets out there who may not have experience in Linux etc...
a) You need to instruct to delete the comments from the replaced lines. This is for non-linux people.

b) I would recommend commenting out the existing items from the hal and ini files and made comments about the replacement items. My understanding this is good Coding 101. And should help anyone reverse engineer the problems.
c) I have MESA cards, and found that the setup of these was best achieved using the MESACT configurator and not the pncconf. NOTE: pncconf taught me a lot about the different aspects of the configuration items, however, MESACT was better for me for a holistic setup for MESA cards IMHO. It allows you to select all of the cards manually and then verify them.
Separately I noted that when I did the configuration this way, I did NOT need to add the GEOMETRY statement. It was not there initially, and not in your files for transfer, and it started ok, no errors. I still need to do some more testing, however, looks better from atm.
So where are we at:
I could start, no errors. Was able to Jog per my setup and return to home easily. The Switch gear seems to work, and I need to sort out how the Axis limits work when I get this onto a machine. I am bench testing atm.
So we are off to a good start.
Because I am completely new to this sort of thing... CNC setups etc.. and CNC machining... What would be a good reference for learning about how to set up a machine, XYZ coordinates, tool offsets, etc.. that would apply to the Probe Basic layouts. This would include how to start off a simple Conversation job.
Thanks again.