You want to get the Y-axis extrusions level, plumb, and at the same height — adjust as necessary to make that happen — flip them end for end, enlarge/drill out holes, shim or machine the ends of the extrusions, &c.
Then you need to get the X-axis extrusion level and square to the Y-axis extrusions — same drill
Then get the Z-axis plumb and square.
The big thing is to work from large to small, outside to in — once you get all the way to the Z-axis spindle carriage plate, it may be needful to go back and start over at the outside — sometimes it’s maddening, tail-chasing stuff, but patience and persistence will pay off.
Once the metalwork is as square as it can be, then the wasteboard can be addressed — you can shim it from underneath if need be, but that’s not usually necessary — then tram it w/ the largest endmill you have taking skim coats — my preference is to mount a piece of spoilboard to the wasteboard and surface the spoilboard all the way to its edges (ensure that it is smaller than the working area).
There is a bit more on this, and some hopefully helpful / explanatory links at: https://www.shapeoko.com/wiki/index.php/Calibration_and_Squaring_the_Machine