help with Marlin re-configure

Hi all. I was hoping someone might be willing to help me re-configure my Marin firmware.
I have a Phoenix 3d printer from EZ3D. It is a pretty good printer, but the software is not so good. I would like to use some of the open source software like Repetier or MatterControl so I can have more control over the slicing process. They said it could be done, but there is something in the firmware that is causing some problems. When I try to print, the printer takes off and wants to go through the roof. Maxes out the Z axis and runs for a few more seconds. Then it appears to start the printing motion while at the max Z
The printer is based on the Mendel/Prusa style. It has 3 mechanical end stops. X is to the right, Y is to the front, closer to the operator, and Z is at bed level. It has a Rambo 1.2 board. The printer limits are 250X215X200. There must be something in the mechanical settings that is making it run crazy.

This is the g-code that their software sends to the printer for homing:
G1 F2800
G1 X400
G1 Y400
G1 Z-400
G92 X144 Y100 Z0
G1 Z200

Maybe someone could look at this section of code and see if they can help.

//===========================================================================
//=============================Mechanical Settings===========================
//===========================================================================

// Uncomment the following line to enable CoreXY kinematics
// #define COREXY

// coarse Endstop Settings
#define ENDSTOPPULLUPS // Comment this out (using // at the start of the line) to disable the endstop pullup resistors

#ifndef ENDSTOPPULLUPS
// fine Enstop settings: Individual Pullups. will be ignored if ENDSTOPPULLUPS is defined
// #define ENDSTOPPULLUP_XMAX
// #define ENDSTOPPULLUP_YMAX
// #define ENDSTOPPULLUP_ZMAX
// #define ENDSTOPPULLUP_XMIN
// #define ENDSTOPPULLUP_YMIN
// #define ENDSTOPPULLUP_ZMIN
#endif

#ifdef ENDSTOPPULLUPS
#define ENDSTOPPULLUP_XMAX
#define ENDSTOPPULLUP_YMAX
// #define ENDSTOPPULLUP_ZMAX
// #define ENDSTOPPULLUP_XMIN
// #define ENDSTOPPULLUP_YMIN
#define ENDSTOPPULLUP_ZMIN
#endif

// The pullups are needed if you directly connect a mechanical endswitch between the signal and ground pins.
const bool X_MIN_ENDSTOP_INVERTING = false; // set to true to invert the logic of the endstop.
const bool Y_MIN_ENDSTOP_INVERTING = false; // set to true to invert the logic of the endstop.
const bool Z_MIN_ENDSTOP_INVERTING = false; // set to true to invert the logic of the endstop.
const bool X_MAX_ENDSTOP_INVERTING = false; // set to true to invert the logic of the endstop.
const bool Y_MAX_ENDSTOP_INVERTING = false; // set to true to invert the logic of the endstop.
const bool Z_MAX_ENDSTOP_INVERTING = false; // set to true to invert the logic of the endstop.
//#define DISABLE_MAX_ENDSTOPS
//#define DISABLE_MIN_ENDSTOPS

// Disable max endstops for compatibility with endstop checking routine
#if defined(COREXY) && !defined(DISABLE_MAX_ENDSTOPS)
#define DISABLE_MAX_ENDSTOPS
#endif

// For Inverting Stepper Enable Pins (Active Low) use 0, Non Inverting (Active High) use 1
#define X_ENABLE_ON 0
#define Y_ENABLE_ON 0
#define Z_ENABLE_ON 0
#define E_ENABLE_ON 0 // For all extruders

// Disables axis when it's not being used.
#define DISABLE_X false
#define DISABLE_Y false
#define DISABLE_Z false
#define DISABLE_E false // For all extruders

#define INVERT_X_DIR true // for Mendel set to false, for Orca set to true
#define INVERT_Y_DIR false // for Mendel set to true, for Orca set to false
#define INVERT_Z_DIR false // for Mendel set to false, for Orca set to true
#define INVERT_E0_DIR true // for direct drive extruder v9 set to true, for geared extruder set to false
#define INVERT_E1_DIR false // for direct drive extruder v9 set to true, for geared extruder set to false
#define INVERT_E2_DIR false // for direct drive extruder v9 set to true, for geared extruder set to false

// ENDSTOP SETTINGS:
// Sets direction of endstops when homing; 1=MAX, -1=MIN
#define X_HOME_DIR 1
#define Y_HOME_DIR 1
#define Z_HOME_DIR -1

#define min_software_endstops false // If true, axis won't move to coordinates less than HOME_POS.
#define max_software_endstops false // If true, axis won't move to coordinates greater than the defined lengths below.

// Travel limits after homing
#define X_MAX_POS 400
#define X_MIN_POS -400
#define Y_MAX_POS 400
#define Y_MIN_POS -400
#define Z_MAX_POS 400
#define Z_MIN_POS -400

#define X_MAX_LENGTH (X_MAX_POS - X_MIN_POS)
#define Y_MAX_LENGTH (Y_MAX_POS - Y_MIN_POS)
#define Z_MAX_LENGTH (Z_MAX_POS - Z_MIN_POS)

// The position of the homing switches
//#define MANUAL_HOME_POSITIONS // If defined, MANUAL_*_HOME_POS below will be used
#define BED_CENTER_AT_0_0 // If defined, the center of the bed is at (X=0, Y=0)

//Manual homing switch locations:
// For deltabots this means top and center of the cartesian print volume.
#define MANUAL_X_HOME_POS 0
#define MANUAL_Y_HOME_POS 0
#define MANUAL_Z_HOME_POS 0
//#define MANUAL_Z_HOME_POS 402 // For delta: Distance between nozzle and print surface after homing.

Thanks very much for your help.

Can we approach this as if it was a new build?

still having issues with marlin? i am currently running marlin on my ramps 1.4 if you want to set up a time to burn some time and melt some plastic i can see what i can do to help.

The attached file is a Marlin build for the EZ3D Phoenix. This build should work with Repetier.

See: " [ez3d.freshdesk.com]" for the printer shape setup.