You can't disable the Estop, or Mach3 will not run. Just set it to any unused input pin number, and toggle the active low setting if it doesn't let you reset.
btw: I just enabled my limit switches, and home switches...now my x axis tries to home to the right (+ side) instead of the home switch on the left (- side) and it doesn't trip the limit switch when it does, it just grinds into the rail.....
when I reverse the homing, then when I jog to the plus, (right) it goes left and vice versa....
I get the abnormal condition light flashing and on the DROs it says my "head" is at -51 inches on a 24" table
This is what happens when you change too many things at one time.
First, you get the machine to move in the correct direction. If you jog to the right, do the DRO's count up (increase). If so, then Mach3 is correct. But if the machine is moving left, go to Config > Homing/Limits and check the reverse box to change direction.
Once it moves in the correct direction, then home the X axis. If it moves the wrong way, toggle the "Home Neg" setting.
Disregard the Abnormal Condition. It's the absolutely worst feature in Mach3. When everything is working the way you want it to, go to the Operator menu, and click "Set Normal Condition". Even better is to remove it from the screen with a screen editor.
There's nothing wrong with the X home switch at the positive end of travel. I have mine setup that way, so that when the machine homes, the gantry is clear of the table so I can setup my parts.
What you want to do, though, is go to Config > Homing/Limits and enter the actual switch position in the Home Offset box. This value is what mach3 sets the DRO's to when you home. So, if you set it to 45, your X zero will be at the left end of the table. When you home, the X DRO will be set to 45.