Z-axis endstop not functioning after Marlin Firmware installation
After gaining more of an understanding of how Marlin works, I decided to look through the  the pins file for the motherboard I am using "pins_ULTIMAIN_2.h".  Sure enough, It had a the wrong pin number for the z stop specified. After changing that number, I gained full functionality.

This is what they should be:

#define X_STOP_PIN         22
#define Y_STOP_PIN         26
#define Z_STOP_PIN         29