"thru-hold". Ooops! 
I think I'm going to move parts around so there are no pins over the USB port. If I were to place a durable layer over the pins by the USB, it would raise up the board way too much for standard headers. They won't mate properly with the Arduino and would be flaky. And long headers would help at a higher cost, but it still doesn't solve for the header sockets for further stacking. But if I get rid of pins around the USB port, I can get away with all standard parts that are readily available.
I can spend time to make it right once and for all, or spend money to work around it for every board. 
Thanks for the suggestions!