Limit switch and E-Stop configuration

I get a few steps forward and despite many searches I can't seem to find what I'm looking for and end up back here.

I have a 7i96 board and I'm trying to get the E-stop and limit switches working. I've wired the E-Stop to +12v into the isolated TB3 input 0, X limit into input 1, Y1 to input 2 and Y2 into input3. I haven't done the Z limits yet because I can't get any of them working at the moment.

In pncconf is as follows:
000 = E-stop, GPIOInput
001 = X minimum limit + home, GPIOInput
002 = Y1 minimum limit + home, GPIOInput
003 = Y2 minimum limit + home, GPIOInput

HAL and INI files attached. Thanks for your help!

What do you have connected to the 7i96 common pin? Believe it is TB3 pin13 or near there. You need to have the reference voltage connected to that pin. For your estop that would be connected to the 12v-.

What type of limit switches? This will also determine how to wire the TB3 common pin. The hal file looks fine.

Ah, so the -12v goes to the common? No I don't have that. That makes more sense. I'm nervous as he'll connecting anything above 5v to this board.

Okay, that got my E-stop working and to a degree the limit switch.

On the X, if I check the INV box and the x isn't touching the limit switch it will home to the limit switch and then I can do nothing more because I have a "joint0 on limit switch error on the LinuxCNC console. If I leave the INV button unchecked I get that error right out of the gate. Any thoughts?

It would be good to have a section on limit switches but maybe I'm just a bigger idiot than others.

Limit switches are wired to the Normally Closed position.

I tried rewiring to the NO positing and unchecking the INV box but I get the same issue. It homes but then stops and gives me an error on Joint0.

I managed to get a working configuration by switching all the limit switches in pnconf to home and not home + minimum limit. Now I don't get the error at least. Is this the way I should have had this all along?