Partially Solved Z axis not calibrated

The printer only knows where the HOME position is on ANY of the Axis (X or Y or Z) by the HOME switches.

So if it thinks Z home is 6 inches in the air then then is where (at least one) of the Z axis home switches tiggered.
They are in parallel, normally open (wired to N/C connector, but then the X axis carriage rests on the switch so that both are OPEN unless you are HOME and the extruder is touching the bed) so when either of them tiggers the RAMPS sees a CLOSED circuit on that Z HOME input and thinks it is HOME.

So, the upshot of this is that one or both of your Z home switches is CLOSED permaturely and it thinks it is home already at that height.

Look carefully at the switches and make sure:

1) they are positioned correctly. The X axis bar should rest on the switches (keeping them CLOSED) when it is 'in the air'
2) the wires are correctly connected to both of them

You might want review these videos:
http://community.robo3d.com/index.php?threads/helpful-videos-novice-expert.7478/

and/or read this thread:
http://community.robo3d.com/index.php?threads/read-me-my-robo-doesnt-auto-level-correctly-faq.4664/

for more details.

 

Adjust the Z offset. The purpose of the offset is to account for machine variations (usually under 1mm).
Add the M565 to your startup Gcode that will account for it.

Also you can play around with where the switches are mounted to the nuts, but I'd suggest the offset instead.