Dumb mistake number whatever. I had a piece of lumber just a bit too long clamped into the spoilboard and went to home the machine. As it moved forward, I heard a clacking noise and noticed the gantry had stopped, because it had hit the board and was stopped! I hit the emergency stop, released the piece and re-homed the machine. A few clunks, and it went forward, but now the right side is back almost 1/2 inch from the left! Not sure where to begin to reset it. Any ideas??
If it were me:
Inspect for damage.
Loosen all the bolts between the gantry and the uprights - just a bit, you don’t want it to fall apart. Just enough so that homing can un-twist it without the gears jumping a tooth.
Home the machine’s Y axis. This should put everything back where it’s supposed to be. If not, manually help it along 
Tighten everything back up again.
Loosen the springs holding the Y drive gears against the rail (or, for non-pro, whatever it takes to “free” the Y motors). This will let the gantry “relax” which may offset it again, which you should check for. If it does, check for bent or warped parts, noting that some offset is normal.
Restore springs/motors.
Home everything again, and redo the “is my CNC square” test in the Avid instructions. You might need to tweak the limit switch positions depending on what might have moved.
I had a similar situation. The y-axis motors became unpaired and I jogged the axis at max jog rate(800 IPM), one motor moved the other didn’t. The gantry was knocked out of square and the motor that moved jumped several teeth on the rack.
1st I disengaged the motors from the rack so the gantry could move freely, then
loosed all the bolts on both of the gantry interface plates and riser joining plates, that the gantry attaches too .
Backed off the sensor flags and pushed the gantry until they hit the bumpers. Retighten all the fasteners, engaged the motors to the rack, reset the sensor flags and ran the squaring routine .
This has happened to me a few times. I just either power down the machine or disable the motors with the switch on the controller to release the tension on the gantry. Then powered back on and re-homed. It never put a permanent twist in my gantry that needed correction.
Wow!! That really makes it so simple 
It’s usually that simple, except the original poster said he tried that already 
Sorry I must have missed that 
This seems to be worse than I thought. I was able to get the gantry back, but now, the motors are not responding. I can start the spindle in mach4, but none of the jogging commands are responding.
The gantry is back in the right place, but now none of the axis motors are responding. I think I may hve screwed up more than I thought.
Try powering down everything (the entire control box) close Mach, power up the box and re-open Mach and home again. As @jjneeb said you probably just need to relieve the tension in the gantry. Mach sometimes doesn’t like E Stops so powering down and back up should set everything straight (literally and figuratively)
I don’t know how that could happen just from an impediment on the gantry, unless it hit a wire. I once had a board vibrate to the side and get caught on the side I had the EStop wire hanging and the board got between my rotary unit and the gantry and pinched the wire so hard it shorted the wires which disables the Estop. Its a good thing I tested the estop after that accident or it would have gotten exciting the next time I really needed it.
The only thing I can think of that would do that is Estop (check your diag window to see if its tripped), or you left your motor disable switch on.