Error messages when trying to run GCode

Ok myself and my partner are totally new to LinuxCNC having worked with Mach3/4 in the past. The problem we are having is that when we try to run a job we get error messages stating "cant issue MDI command when not homed.We first load our GCode and home the machine (front left of machine as your looking at it), we then move to the spoiler board just in front of the stock lower the Z axis to the spoiler, hit the touch off button put in -25.0 as our stock wood is 25mm thick, we then raise the Z axis and place it on the stock with the Z resting on the wood we then hit touch off for the Y and X axis leaving it at 0.0 and we use P1 G54 on all three axis. When doing the Touch off screens each time it sends up this error message, when we try and run the programme we then get the message "Program exceeds machine maximum on X, Y and Z. I'm hoping someone can enlighten us as to why this is happening is it something in the stepconf or INI file we have overlooked.
Many thanks in advance.

Here is the INI file. I will just add that we are using a Mach3 BOB as we are unable to get a Messa board at the moment due to stock. The other thing to mention is that we had to invert both the Direction and home for Y and X axis to get them to travel in the correct direction and home to the correct place.

HAL Files

I have tried to do this prior and we get the same error messages. And the erroring appears as you press ok on the touch off box. Its very strange i do wonder if its the board as we couldnt get a Messa board (they are out of stock) we have used the Mach3 BOB

Thats interesting on our GUI we have a button that says "home axis", and i have to home individually each axis. On videos i have seen the same button says "home all". Is it possible to add this line and exactly where do i add it?? or do we need to download the whole program again.

Thank You