After fighting with this for the last few hours, I'm going to ask for some ideas.

Right now I am having really bad serial communications problems, often the board just randomly hangs and does nothing. It seems like there is some sort of power/ground/signalling problem as if I touch the board with my finger sometimes it starts transmitting again, sometimes it resets.
It always seems to make it through the waypoints though.

....252 Lat: -1 Lon: -1 Alt: 65535
253 Lat: -1 Lon: -1 Alt: 65535
254 Lat: -1 Lon: -1 Alt: 65535
255 Lat: 10495 Lon: -256 Alt: 65535
and then it just stops, but it stops in a random spot each time.

This is my hardware setup and I am using kermit on Ubuntu to receive serial data for testing.

I am running in NEMA mode and
#define FAKE_GPS_LOCK 1

Where could the problem be?

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It's impossible to understand your setup from that picture. If you decide not to use ArduPilot as directed, any number of things could go wrong. For starters, you're not using a RC system for power. Do you have some other regulated power source?
Why have you separated the Shield from the Ardupilot? Also, you do not appear to have the GPS plugged into either the Shield board or the Ardupilot in your picture.
So how is the Ardupilot communicating withe the GPS? Without the GPS, the Ardupilot will try to perform "fly by wire". However without and input on the CNTL input to the Ardupilot the board could be randomly bouncing between Manual and RTL/WP.
I suggest that you put a Servo Driver on the CNTL input so that you can control the Ardupilot mode and try hooking the GPS to the Ardupilot.

Just a thought.

The protoboard has a +5v switching regulated power supply.
The power is connected through the power and ground of the servo connector but I am having similar problems when connected next to the ftdi cable. but it seems to work a little better.
So I guess the problem is power related. It is weird that sometimes it continues right where it left off when I touch it.

I will try running it off a battery and a 7805 voltage regulator next.

There is no GPS connected since I am trying to debug a GPS emulator.

It's almost working but I'm having a problem with my checksums matching and the serial port acting up is driving me crazy trying all day to debug it.

The board at the bottom of the image will be the serial GPS emulator that plugs into the shield.
It's kind of hard to really know from the could be number of the only connection between ArduPilot board and your GPS emulator board serial connection? If so, try having common ground between two boards and see if that helps
Are you using our code? (2.3). If so, as Tom points out it won't work without RC inputs.
Agree on that. You need a common ground between all these elements.

I'm not even sure why you're using ArduPilot for this. Why not use a regular Arduino board if you're not using the RC or GPS elements that make ArduPilot unique?
Thanks for all the help, it looks like it was the RC inputs bouncing around. It has been working flawlessly once the receiver was plugged in.

I am using the 2.3 code but I'm planning on updating to 2.31
Now I just need to get the rest of the HITL setup working.

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