Thanks for replying. I checked the wiring and it was ok.
But I looked through the forum and found this related post. x axis now running in reverse direction
After reading the last post on that thread, I checked my X axis belt and compared it with the installation instructions. Yep, I had re-installed it incorrectly. 
After that, when I did Autohome, the X axis started moving to the left towards the limit switch. And it stopped when it was supposed to, along with the bed on the Y axis. Then the Z started to move down towards its home position.
But when the Z got closer to the bed, something happened. The left side started making some grinding noise and it became out of alignment with the right side. The left side became lower than the right side. I had to turn off the machine. It didn’t get close to the Z limit switch.
I ran some tests with moving the Z up and down. I put a level on there and it stayed level in the middle. I tested the Z limit switch manually during an Autohome operation and it was working fine.
I did have to take the machine completely apart in order to replace broken pieces. Maybe it is something with the couplings for the Z.
Any ideas?