In your original pic of the cut parts the notch where the depth changes is a classic sign of machine flexure. I had the same thing with my machine till I beefed it up. If I were a betting man, I'd say your gantry sides are flexing and also the z axis is either flexing itself or flexing where its attached. I suggest that you examine each park in turn while cutting and identify the problem. As JAZZ mentioned, check the couplings too.