I’m really hesitant to use the word, “level”. I imagine someone using a contractors level on a machine, and it’s not nearly a precise enough instrument to get the kind of accuracy we’re looking for.
I think “flat” is a better word. It all starts with the base of the machine being “planar”.
That being said, I did level my table. But only because I did an epoxy pour with the job on the machine and the epoxy ran to one end of the job. My table sits on a garage floor, which is graded toward the front.
So, NO. Your workbench not being level should not be a problem. But starting with a flat surface will make things easier.
None of that matters concerning the problem at hand! If your machine has not been calibrated, it would only affect the size & squareness of the job, but it should still be smooth.
I would look at Kevin’s suggestions, particularly on the Z axis. I just recently had the same problem & had to remove the Z axis coupler, clean everything, reassemble it and tighten the set screws in the coupler. Although in my case the Z axis was creeping downward & did not go back up. So it just gradually kept removing too much material.
It make sense, a month ago my machine was cutting perfectly. Then I noticed a line in my project and little by little the lines in my projects have increased.
The machine is in the same place it was a month ago when it was cutting perfectly.
I also have a Shapeoko Pro XXL and although we have linear rails I’d still check if it’s sound mechanically. I’ve noticed in the past some of the bolts securing the rails getting loose so part of the maintenance routines when I clean and oil the rails I also check the bolts securing them to the machine.
If you notice the symptoms more when doing 3D files then that is possibly a hint that it’s something related to the Z-axis.
Edit: just read complete post and you indicate checking all screws so that rules out bolts on linear rails. @woodworm already pointed out the set screws on the Z axis which is certainly worth investigating.
I also remember someone on the forum having the bolts securing the block on the z-axis ballscrew/leadscrew coming loose from the plate that the router/spindle is mounted to. You can probably check this by grabbing the router/spindle and trying to wiggle it up/down and see if there’s any visible movement or sound being generated.