Thought I would chime in with some observations and gotchas before they bite someone else.
First, a reminder (I guess I forgot this) that TH pads on Layout appear on the Mechanical Layer while surface mount pads appear on either Top or Bottom Layer. Through me for a loop as I often shut down the Mechanical Layer to keep the Layout cleaner for design. Imagine my surprise to see (rats nest) wires running all over the place and terminating in thin air!.
Second, I noticed some odd anomalies in the 3D view. Was reminded by staff at Sunstone that 3D is really a work in progress and the bright copper pads on the attached file are simply artifacts and do not really represent anything.
Will report more when I am finished with latest 5.1 design in a few days, hopefully.