Homing not working but E Stop In is ?

This forum has to be the most helpful and friendliest I've ever been on and Andy, really is a legend. He's tireless, helpful, makes you think and is happy to help anybody. I started my CNC journey with an Aduino too by building a rotary table controller.

Master is the unstable development branch which will become V 2.8. Version 2.7 is the current stable release. I think of a joint as being a motor (there can be multiple joints in an axis - eg on each side of a gantry or maybe the Z on a knee mill where the motors on the knee and the head add together on ths Z axis).
Up until V 2.8, with trivial kinematics machines (eg conventional XYZ mills, lathes and gantries as opposed to hexapods and robots), there was a 1:1 mapping between the axes and joints (X=joint 0, Y=joint 1, Z=joint 2). That means you can home a joint and the matching axis will be homed which is how you have set up your control panel so don't dismay!

Before I started with LCNC, somebody wrote a better Joint Axis module (JA) which has now been merged into the 2.8 branch. This made changes to the homing sequence to simplify squaring of a joint axis gantry. It also removed the 1:1 mapping between joints and axes. So now the X axis could be Joint 9 if you wanted. This had some additional side affects the developers missed but I think most of them have been fixed in the last couple of months.

I've had too much to learn to learn much about Gcode yet, but I think there is a way to set the starting point of a part similar to how you envisaged you would set a home position. Maybe somebody could chime in and explain how to do that.