Populated the PCB using a solder iron opposed to paste. This is why I had chosen the larger packages though you can still hand solder the smaller ones but they are difficult. The best video on hand soldering I have seen was by Ladyada from Adafruit. Her videos are the reason I got into surface mount. Looks so intimidating until you do it.
OSHPARK PCBs only come in two thicknesses and they are not thick enough for a USB slot. I glued a spacer on it to make it fit. I have used Elecrow before and they are almost as good as OSHPARK and a lot cheaper but takes twice as long to deliver. For small PCBs, OSHPARK is the way to go. The piezo is partially under the battery holder. I think it will be OK but probably not good for manufacturing. I have not soldered the crystal because I am waiting on some to be delivered. I had soldered a standard header to the programming/test port but it was actually intended to be an edge card type interface. Waiting on those also but that is OK. As long as I can test it and get it up and running then that is all that matters. Especially when I know I am already going to change some things on the board but it is good for now as a proof of concept.