So here is your post processor back with the changes, "EXCEPT" for the G53 Z0 value that is causing your stock gouge...
Line 5 in your post has this:
For us, we put a G54 X0 and Y0" in the place of the 2 G53's.. The program itself will output the set rapid up as it's last command, then the machine will zero to X and Y 0 at that height...
5. End of file for non-zero tool
If you know what other value you want to put there, that is the change you need to make. But if you are not using work AND machine coord systems, then you need to be careful about putting in a hard coded Z value in there.
Let me know if you want to get into it any further.