Sorry I've been a while replying.

Unfortunately, my router PC failed to install a recent Windows 10 update and I ended up having to reinstall Windows, etc. That was the point when I found that I had not taken a backup of that UCCNC configuration, so I am going to have to start again from scratch.

Despite all that, I don't think that the pins you use for step and direction outputs matters, as long as you do use "output" pins! Having connected everything, you then tell UCCNC which ports and pins you have chosen - unlike the cheap breakout boards, where XYZA connections are typically dedicated. Connecting the limit switches, etc, you can use the diagnostics screen to see which pin triggers when you operate the relevant switch manually and then tell UCCNC which is which in the configuration page.