Good work, phones do make a good inspection mirror, for when you don’t have an inspection mirror.
If you think that clean, warm, dry access to socket head screws is bad, then don’t work on a vintage British car. The apparent design objective on everything British Leyland, Jaguar, Lotus etc. was that all key fasteners should be accessible only by touch, to a mechanic whose anatomy includes a hand with at least two thumbs attached to a 6 foot long arm with 3 elbows.
It is but a mere scratch. I’m sure someone here could make a bracket or a widget to hold the wheel a little straighter, but that aside, T-Cut and gaffer tape
Did you check that the moving Z carriage is vertical about the X axis as well as about the Y?
As for unwanted holes in the wasteboard, I have found that using the Shapeoko to open them up to a standard dowel size and then just gluing dowels into them works nicely if you’re coming back with a levelling pass. A single program which makes a, say 1/2" hole about the zero point works nicely for this.
I’m still chicken and using aluminium dowels so that when I crash a cutter into them it just makes a different noise and I have a shorter locating pin.
What remaining problems are you chasing ? That surfaced spoilboard looks infinitely nicer to me that the original pics you posted, and MDF being what is you will never get a completely even look over a surfaced area. Do you feel the tool marks with your fingers or it just just the look ?
I would suggest you go ahead and try milling a large pocket in (actual) wood, with a typical 1/4" cutter, and check whether you see any tramming marks on the bottom of pockets?
I use a pocket, wider and taller than 400X350 by [one cutter diameter + a little margin], to be sure that the center of the cutter will travel up to the edges (and little bit over)
Stepover: 40% is typical, but it does not matter much here
Adaptive toolpath: don’t bother for now, it’s not supported in CC anyway and is mostly useful for metal. But if you are interested I wrote a small bit about it in the ebook
It has a lot of trapped and unrelieved stresses, and after you surface down some arbitrary amount, it can just start to warp. I typically see the edges lift, while the center remains low. Might not be a big issue in your case, as its a 16x16 size, but seeing as you have no clamping attachment (only alignment pins) this might bite you in the keester.
IME once the warp has started, no level of surfacing is going to redeem that spoilboard.