Here are the two saved recommendations from the tech support queue:
Squaring Gantry to Front/Rear Plates
Loosen all of the screws that hold the gantry together (4 on each side), these should still be loose from the initial assembly.
Loosen the screws that hold the Y axis rails in place (16 total). These should also still be loose from the initial assembly.
Slide the gantry to the front, so both Y plates are touching the front plate.
While holding the gantry against the front of the machine tighten the front of the Y rails (8 total)
Now - systematically begin tightening the 8 bolts on the gantry. Work your way from left to right, going back and forth in a X pattern (similar to tightening the wheel of a car).
After the gantry has been secured, slide the gantry to the rear of the machine and tighten the 8 screws while keeping the gantry pressed against the rear plate
Glad you’re making progress!
Being out by as little as 1/16" is about 1/10 of a degree — take out any unsquareness remaining after the above you’ll have to do one or more of the following:
- clear the powder coat out of the holes
- drill out / enlarge the holes to allow for adjustment of the plates
- shim the ends of the extrusion
- file / machine then ends of the extrusion flat
There’s some discussion of this, and a number of links at: https://www.shapeoko.com/wiki/index.php/Calibration_and_Squaring_the_Machine
That said, if you can get this to occur at the back left corner of the machine it won’t interfere with homing, and so long as:
- the bed is level
- the extrusions are level to the bed
- the Y-axis extrusions are parallel to each other
- the X-axis extrusion is square to the Y-axis
- the Z-axis is plumb and square
the machine will run true to itself and cut squarely (given the proper toolpaths and feeds and speeds).