Joint limit switch errors

This is not a quick reply and I am sorry for that. I worked with what you gave me and made a lot of progress but then I have been away until today.
And I thank you for what you sent. I was at the point of trying to home the Y axis and needed to try to find out how to manually home it but then suddenly I got a strange problem and was working on that when I gave up before leaving. Suddenly two joints were flipped; that is, when I tried to work the Z axis it ran one of the (paired) Y joints.
So that is where it is now, of course, and I will work on that today for a while and then have to leave again for a few days.
Thanks again to you. Nice to talk to someone (that I assume) is from the British Empire. I worked for many years in Europe and part of that time was in Scotland, England, and Ireland. I have ties there still.

It would help if you posted the config files ie. ini and hal that you are using.

This is not a prompt reply and I apologize for that. I thank you for your taking the time to help me.
I had your reply first of two replies to my last post and looked at your first, and looked at the links to the commit and the buildbot errors but did not make any progress there because of my ignorance, no doubt.
. And I looked at the other links to documentation and they were what I had been using to try to solve my problems. And failing there.
I had another response from someone who had patched up my .ini and .hal and when I saw his corrections I made some sense out of the instructions but also saw that I never would have figured out the problems strictly from the written material.
So I worked with the patches and made a lot of progress but then had to leave until today with problems still remaining. I will try to fix those.
Thanks again for your help.