Ok, need some advice here. Last night was working on a tiling idea on a full 4’X8’ sheet of 1/4" MDF. My sone was here and things were going pretty good until it got to the right side of the first tile. The dust boot started coming off and I held it in place and my boy hit the stop instead of the pause.
I thought no big deal, will just edit the gcode to skip everything up to the stop point. Only I forgot to put in a start point with the Z up 
Upon running the gcode the spindle pomptly went to it first point and ramped down into the stock at the wrong spot. I hit the emergency stop and fortunately the spindle was in the middle of a cutout piece.
It was getting late so I just left the machine off and was going to deal with it this morning.
I noticed the error in my edit and added in the correct start point with the Z up before the ramp down and ran an air cut after rehoming. The spindle was off on the Y by about 3mm. So I rehomed G0 X0 Y0 Z1 when I noticed the spidle was not where it should have homed. The hole was drilled from a previous homimg and any attempt to set the Y (or X) results in a limit error.
Trying to move the Y -1 mm GO Y-1 results in the error:
"Y axis position -1mm is less than minimum soft limit 0mm
While executing GCode block:G0 X0 Y-1 Z0 A0
At: :4
Caused by: Y axis position -1mm is less than minimum soft limit 0mm"
If I try to tell the machine it is at 1 mm with G92 Y1; G0 Y-1 results in limit error.
So what to do?