Whenever I setup to run a new cut, I will jog the axes to my zero point on the stock. However, when I run the gcode file, it will always jog to some other location unless I use the “set home offsets” command. Shouldn’t a G92 command program it’s current position as 0,0,0?
Also, if I set the origin programmatically, can the G28 home command move back to this set position?
I can upload a sample gcode file if requested
I usually just hit the reset button on the arduino, fastest way for me to reset all the axis to zero.
Yes, a G92 X0 Y0 Z0 is a good way to reset the origin at the stock after jogging to it. I just put it in my post file. Below is an example of the first few lines that come out of Fusion 360 and the postprocessor I use. I used to cycle the Arduino power until I realized that G92 was easier. Also note that I change the stepper disable timeout to give me time to change end mills between operations.
Steve C
;T2 D=3.175 CR=0 - ZMIN=-2 - flat end mill
;T3 D=3.175 CR=0 - ZMIN=-10.4 - flat end mill
;T5 D=3.175 CR=1.587 - ZMIN=-14.061 - ball end mill
N10 G90
N15 ;Units in mm
N20 G92 X0 Y0 Z0
N25 M84 S1800 ;Change Stepper disable timeout to 30 minutes
N30 G1 Z5 F2000 ; Lift Z 5mm to avoid dragging to first operation
;Face4
N35 ;T3
N40 M106
N45 G1 X77.064 Y1.444 F2000
N50 G1 Z15 F2000
N55 G1 Z1 F2000
N60 G1 Z-0.683 F1000
…and no… I think that G28 will look for end stops to home to. If you want to go back to the origin then just use G1 X0 Y0 Z0, right? I don’t think end stops are very useful for a CNC other than for safely stopping on running bad G code or the wrong G code. I’ve never run the wrong g code file of course 
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I really like having the endstops. They make it easy to get a reproducible zero point. I mounted mine on clamps that are easily moved - there are pics in some of my other posts. I have occasional problems with the machine losing registration from dropped steps (usually binding on the z lead screw, I think), or having the power fail - that one doesn’t happen as often, now that I plug the router, shop vac, and ramps into separate plugs/power strips.