I just built a new stand for my Shapeoko. When I was moving it on, I moved the x axis all the way forward and found that the gantry does not touch the front on both sides. Here is a shot of the left side.
Check the opposite extreme of movement, there are three possibilities:
the Y-axis rails are unequal in length and this is caused by that (early machines had rail ends cut by the extruder, normally this is quite square/even/equal, but not always — this is why we now have a CNC machine large enough to machine both ends of a rail)
the Y-axis rails are equal in length and the rails/end plates are shaped as a parallelogram
both the Y-axis rails are unequal in length and the rails are not square
In my experience, the best approach is to work from large → small:
level the table (optional, put a sheet of foam in-between the table and the machine, dampens noise/vibrations, makes leveling easier, addresses sag on larger machines)
ensure that the end-plates are level
Y-axis rails level and parallel to each other and plumb/vertical
gantry level, square to the Y-axis rails and plumb
