Your E-Stop LED is lit so it is that that is the problem, Either you have the active state of the E-Stop setting wrong , you have the pins set incorrectly , your wiring is wrong or your E-Stop button is pressed.
You do have the Home switches active so likely you have the active state for them set wrong.
Hood
I cycled my EStop button many times, and it isn't on. I even opened up the case to see if something was unplugged or broken. I didn't see anything. If I do press the EStop button, my controller powers down, so I think the switch is working correctly. I toggled the EStop active state, and nothing changed. I did notice that it toggled it's self back to how it was before I toggled it... I'm not sure why it did that... is that an xml file thing?
Is it possible that the xml file doesn't save all of the settings Mach3 needs for my controller and machine? If it doesn't, I guess I have to figure out what they need to be, all over again.
If I "correct" the error buy clicking the "fix it for me..." button, and I tell Mach3 to reference, the Z axis display on Mach3 increase indefinitely, as if I had an infinitely high Z axis, and it never gets to the limit switch.
I still wonder, if it's a limit switch problem, why the steppers don't even power up. When I first set up Mach3 with my controller, they powerd up, and I just had to get the Ports & Pins all set correctly for it to see the limit switches.