That firmware is not customised to be used for the solidoodle workbench.. theres a couple more things that you'll need to change. Specifically, for the z-axis problem, it will be the pins.h file. The post and thread in the link above should help you out.. it looks like you'll need to get the original pins.h and copy it over to the new firmware youre putting on

#define X_STEP_PIN          0
#define X_DIR_PIN           1
#define X_ENABLE_PIN       39

#define Y_STEP_PIN          2
#define Y_DIR_PIN           3
#define Y_ENABLE_PIN       38

#define Z_STEP_PIN         24 // PD0
#define Z_DIR_PIN          27 // PD3
#define Z_ENABLE_PIN       26 // PD2

#define E0_STEP_PIN         6
#define E0_DIR_PIN          7
#define E0_ENABLE_PIN      19

#define E1_STEP_PIN         4
#define E1_DIR_PIN          5
#define E1_ENABLE_PIN      23

#define HEATER_0_PIN       21  // Extruder
#define HEATER_1_PIN       20  // "HOTBED"
#define HEATER_2_PIN       -1
#define HEATER_BED_PIN     25  // PD1
#define FAN_PIN            16  // Fan
// You may need to change FAN_PIN to 16 because Marlin isn't using fastio.h
// for the fan and Teensyduino uses a different pin mapping.

any help would be greatly appreciated.