This is theoretical assumption, but I suppose that your steps/mm values are now wrong in EEPROM - specifically they are set to 0 (zeroed steps per mm)? Could you please use LCD and navigate to Configuration > Advanced Settings > Steps per mm and check what values are set there? If there are zeros, could you set them to positive values (e.g. =80) and ...
For both machines did you compare extruder's (E) steps/mm setting in Marlin and possibly stored in EPROM (so check from the LCD in Configuration>Advanced settings) ?
Also stepper motors ... I believe they are exactly of the same type? There are 1.8 degree and 0.9 degree stepper motors on the market - so exactly doubled flow could be related to rotation. ...
The supplement on how to proceed with custom menus in practice:
Enable (uncomment) this line in configuration_adv.h:
Below there are 5 sample entries, later you can change them or remove/comment out.
You can add new, for example:
#define USER_DESC_6 "Home Z (0.2)"
#define USER_GCODE_6 "G28 Z\nG0 Z0.2"
The MKS Base v1.2 is basically an Arduino MEGA2560 and a RAMPS1.4 on a single board.
You can use the RAMPS pin designation.
Note that the endstop to origin distances is explained in question How to center my prints on the build platform? (Re-calibrate homing offset).
In Jims Marlin fork you can find this at:
#define X_MIN_POS 0 - XTRA_BED_LEFT
You do a critical error in your order of operations: you home. Then you home again.
However, the firmware does not check if the switch is already depressed, it waits for a signal to cut out. But the signal is already not there. And as you will notice, it moves into X+ and Y+ before rehoming into 0, but does not do so in Z.
To prevent that behavior, you need ...