"Ref All Home" is *not* meant to zero the axes when you jog to your work piece. That is what the individual "Zero X", "Zero Y" and "Zero Z" buttons are for. You should only do the "Ref All Home" one time after starting the machine and Mach4, and that should be done with the axes jogged near the limits of travel, and at the position on which you base the soft limit settings. This sets the "Machine Coordinates".
Then, jog to what you want to be the zero reference point of your work piece (i.e. where ever the GCode file considers (0,0,0)), then click on "Zero X", "Zero Y" and "Zero Z". This set what I call the "user" coordinates, which are used for the GCode file movement. This will NOT change the soft limits, as they *always* are in "machine" units. It may *look* like it changes the soft limits.
For example: You jog near the lower left corner of your usable travel and click "Ref All Axes (Home)". The DROs now how all zeros (presuming that your "Home Offset" is zero for each axis). At this point, the machine units and user units are the same.
Now presume that your X axis soft limits are 0 to 10. Mach4 won't let you jog beyond 0 or +10 in either machine or user units (because they are the same, so far).
Now, jog the X axis to 1.000 and click on "Zero X". You are now are 1.000 in machine units and 0.000 in user units. The soft limits are still 0.0 to +10.0 in MACHINE units, but in user units they are -1.0 to +9.0. You haven't actually changed the soft limits. You've just shifted the user units.
OK, now on to your real question: "how can I relocate the shape within the given coordinate"? Does the Mach4 toolpath display show your shape starting at (0,0)? Or is it offset from that? If it is offset (i.e. not starting at 0,0) then you need to figure out where the GCode file thinks zero is relative to the shape. Or you can use probing to determine work offsets. This is beyond my knowledge. I suggest you start another thread (i.e. new subject, something like "how do I set work offsets") and hopefully someone else will respond.
Bob