Skewed lines, shattered faces, and hairy circles. What's going on here?

Lesson learned, it is. Started over with all measurements being scaled x1000. Those dots showing up at vertices are what I’d like to prevent, particularly on the circles. It becomes impossible to select the entire circle’s circumference, (unless there’s a trick I haven’t learned yet).

My new and improved model has been near flawless - until one of the last operations (still scaled at x1000 from the begging).

As seen, I select this center bore circumference so that I can pull down to create a chamfered edge. The picture I’m posting doesn’t show my cursor, but it is on the highlighted circumference with the “move” tool and the down arrow key depressed to constrain movement to the blue axis.

I pull the circle down, and once I click to set it, the dots at the vertices show up again with a couple gaps/missing segments. You can also see some strange lighting showing at those gaps. I’ll try redrawing those circles using fewer segments to see if it helps. The diameter of that highlighted circle is 632". No segment should be anywhere near 1mm.

Hidden geometry