Looks like the missing parts were errors on my end (go figure). The common mode filter for USB was out of stock and I didn't select a suitable replacement (which was available). The switches were in the CPL file, but not the BOM so they won't be placed. I've ordered the balance of parts from Digikey and should be able to finish off the boards by hand. As of this morning the PCBs are almost done with production. I've updated the schematic with part numbers from Digikey for all the parts.