My first problem was setting the wrong Z dimension in my original file. I had Z=0 at the bottom of the part, not the top. This caused a lot of confusion with setting the zero point on the table, and I ended up using an offset to get things right. However, I was guessing at it, and may have been off in my calculations a little.
My second problem was not tightening my collet enough to hold my endmill. I thought it was adequate, but my depth kept changing during my second cut, and when I stopped the tool and checked the tightness, it had loosened a lot.
My third problem was holding the wood to the table. I'd used the composite nails to good effect, but with a couple of false starts, my final work was far enough down on the wood to be beyond my last nail. I think this was responsible for the exterior cut gouging the surface a little. Fortunately, it was a small cut and the TechShop DC gave me a pass, but I really want to avoid this problem in the future.
My last problem was using too high of a plunge depth. I had to adjust VCarve Pro's tooling database to add the 1/8" endmill I was using, and while I correctly updated the diameter, I forgot to update the depth, and I think that let to too deep of an initial cut which then led to having the uneven bottom surface.
My final part was OK, but it will need a bit of manual work to clean up parts, and I already had some chipping from the pine in part of a relatively thin interior wall.
1) remember to run VCarve with Z=0 set to the top of the part.
2) when adjusting your endmill settings, make sure you adjust all of the parameters
3) when using natural boards, it's probably a good idea to plane them first to ensure a uniform thickness
4) when affixing the board to the surface, go a little overboard with the composite nails. Why use four when six or eight would work?