New 12" user and I am LOST!

[printbus]

As for the LCD movement, Collin told me not to use that as it can get the Z axis out of sync. I just can't figure out why it homes to a different z position when I hit autohome? SHouldn't it always stop when the endstop is activated?

I've never heard of using AutoHome on the LCD causing the Z axis to get out of sync, and that makes little sense. You are right - unless there are wiring shorts or other issues, the final position of the all axes after a home action is driven by the endstop switches.

The MakerFarm printers are only equipped with endstop switches at the minimum positions. There have been variations of Marlin around that have the inputs for both the minimum endstops and the maximum endstops enabled. In a few cases, there have been issues with the unconnected maximum endstop inputs floating to an active state and being detected by the electronics. Whether that could be applicable to your case, IDK, but it'd be something we could help you look at.