Linuxcnc error

I commented out the lines your highlighted in the orac Hal file and left the others in the custom Hal file.

But I'm still stuck at the home pin doesn't exist. I've commented it out to see what error was next and noticed it was an error on z motor, these lines where commented out in the x motor lines so I did the same. Next error after that is the z home pin. I'm just so baffled. I've looked back in the Hal file and there allocated to pin 19 and 20 which is correct and the right way round also. everything I'm told make sense but I don't have the knowledge to look through the files and work out what's right and wrong.

What version of LinuxCNC are you running?
"joint.0.home-sw-in" will only exist in version 2.8 (the development version)

It is Linuxcnc 2.8 I have. That's what come on the machine

Could it be a firmware issue with the mesa boards?

There have been some improvements in noise immunity
in the 5I25 firmware if you have firmware more than a couple of
years old.

This might affect the 7I76 card detection (and therefore 7I76 signals) if there's
a noise issue in the DB25 cable, but note, this cannot affect the missing
joint.0.home-sw-in pin. This indicates that either you are not running LinuxCNC2.8
(it is possible to have multiple versions on one system) or perhaps that LinuxCNCs motion
module did not load for some reason

You should really check the connections and power supplies in the machine. Way to many things missing. Check if all the switches are geting power if they should, check the power supplies for stable voltage or voltahe drops or when starting Linuxcnc if any power supply turns off for a moment as the other electronics are activated, etc.
Also check if the connectors on the Mesa board are correctly inserted on their respective places.