(B) No my spoiler board is not machined flat. I will order the bit today…thank you.
This is not at the 1/16" level but it is a good thing to do as it ensures the best outcome… you’re taking things as far as the machine can. 1/16 = 0.0625". Your SO3 is capable of much better than that when properly aligned, tightened, and tweaked. Something on the order 0.006 would be more like it.
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but noticed the border is sightly out of square which tells me something IS out.
Please report back on your checking and potential tramming (squaring up) your machine.
With a new build, there are plenty of things that can be “off” and need adjustment. Check squareness and depth at the center and four corners. All five should look identical and be “exactl” what one expects.
(C) The wood measures pretty good and consistent.
That’s good… but don’t count on it from all sources of hardwoods. Some sources provide beautiful wood with amazing variances.
(D) I did have the stock tightly secured. Did a test piece yesterday with the piece not has tightly secured as it should have been…what a mess!
Just checking! 
You’ve had the joy of a fixture coming loose and stock moving. Been there! Done that!
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