Wow those are all great suggestions. I will add debugging flashes the next chance that I get. Also the capacitor you speak of (Nick Gammon) is a 10 microfarad. I didn't know exactly how to type in the character "µ" into eagle at the time. Also I had never thought about bypass capacitors (in fact I just figured out what they were). I will add those to the 328, xbee (it is on the xbee adapter from adafruit though), and on both ends of the wires to the outside board. The final length of the wire that connects the two boards will probably be about 5 feet and will need the capacitors for sure. Also I will include them on the rfid reader on the outside board (it is shown as 2 headers on the schematic but is really the id-20 rfid reader). Hopefully that will clear up some of my problems. I will try it out and reply as soon as possible about how well it works.