@phaedrux @fcwilt Got it, I can adopt this homing with two speeds, it might be useful since the machine is quite big, etc.
But I have good news, our team has been working here since Friday trying to find the problem and we did it. The y-axis rods were slightly bent, which made the X-axis twist,
which consequently changed the distance between the nozzle and the Z-Probe along the X axis. Before, we had no problems with this slight misalignment because we didn't use a Z-Probe, and that's why it took us a while to check this alignment.
Finally, thank you very much for your help and attention, I learned several new things in the process. Case closed.