I finally fixed the short! After lots of reading about freeze spray, IR cameras, finger testing, etc, I finally followed the intimidating advice to hook up some current and use a multimeter to find where the smallest voltage drop was. In my case, this meant about 1.5 A of current hooked up to the VCC and Gnd Pins. Then, because I was pretty certain the short was below one of my ICs, I just measured the voltage across each corresponding capacitor. The MCP chip I set up to handle LEDs had the lowest voltage drop and when I popped it off the board, sure enough, there was a giant solder bridge below the chip out of sight. I fixed that, and now I can talk to my MC when it's plugged in to the shield! I'll be posting about my further debugging over the next few days/weeks.
A quick soldering retrospective: like a lot of people, I was intimidated by switching to surface mounted from through hole devices. I agree with others I've read that this is a bit silly. Soldering smaller smd components is not a huge deal. In some cases it's easier. That said, I wish I had avoided .5mm pitch components when I could get away with it: they are much harder to trouble shoot and solder than the bigger surface mounted devices.