Strange Gantry Squaring/Homing

Hi - I've gotten Linuxcnc to work well on several machines but each time the machine wasn't constructed with enough precision to make it reliably work the way I wanted.  On this machine I finally built it the way I should have.  I used the files from my old machine and adapted them to this machine If something is commented out it is because I haven't got to that yet.  The machine moves great and the X and Z axis move and home really good.  The Y axis moves good but I can't get it to home properly. If things are set up so that each axis has a pnp sensor on side will respond to the sensor but the other side will turn off the led acknowledging it should home but it keeps moving towards the sensor.  If I tie both sides to a single side it works as expected.  This is fine but it prevents squaring.  I've included my files so maybe somebody could see where I've gone wrong.

Both joints of a gantry need negative home sequence numbers,
but your ini file has a negative and a positive:

[JOINT_1]

HOME_SEQUENCE = -3


[JOINT_2]

HOME_SEQUENCE = 3

Thank you for getting back to me. That had already been changed in the original file but I forgot to change it in what I posted online. It still has the same problem. Currently it is on joint 2. The constant homing issue has left the gantry a little out of square. It seems like whichever side is closer at the start has the problem

You  might do a halscope plot of both limit switches and both joint positions
when homed to get a better idea of whats going on.

To square add HOME_OFFSET to your ini. If you are 2mm out of square, the difference in this value needs to be 2mm

Thank you for the tip about using offset to square it up. I was never really sure what it was used for. One of the things I added to this machine was adjustability. I'm sure glad that I did. I worked on it a bit getting it back to square and it's now within .5mm. I'll use the offset to get it the rest of the way. I would like to get auto square working. I've confirmed the inputs and the state of homing using halshow. I've never used halscope before. Do I set it up like halshow? What should I be looking for? Thanks both of you for the help!

I would just edit the ini file but that means you cant use pncconf or stepconf again. be sure to read ini file docs and homing configuration docs