The power is being supplied via the on board 5v pin.
But what is supplying power to the board? Is it the USB cable? A battery? A wall wart? Does the radio transmitter have a separate power supply? Do you have a schematic/drawing for the entire system?
it should be able to handle 400mA... the normal I/O pins can handle 40 mA per pin.
That is the Absolute Maximum current that can pass through the Arduino board or a single pin, not the capacity of your power supply. If you allow any more than that, you'll let the magic smoke out. 
I'm assuming the 4 bit sound card is well under that current ceiling.
Not necessarily. Is the sound card in a PC or is it a stand-alone module? If it's inside a PC, it's using the PC's power supply. The capacitors on the AUDIO and MIC lines prevent the Arduino from drawing any power over those pins (mostly).
If it's not in a PC, and the sound card is connected to the same power source as the Arduino board, look at the specs for the sound card to get the power requirements. Or tell us which sound card you're using.
If you have speakers and an amplifier using the same power source, you need to include that in your power calculations, too.
BUT when the GPS does have fix, and when the packet is being sent to the [radio?] it stops mid way though the packet transmission. About the same spot every time
That still sounds like a power problem, but it could be an electrical noise problem. How close is the transmitting antenna to the board? This is why we need a complete description and/or pictures.
Have you tried level-shifting the GPS RX/TX pins yet?
It could be a code problem, but I've tested the sketch with commands and GPS. I have assumed that LibAPRS is ok, so maybe I should look a little closer. Just to be sure, from where did you download LibAPRS?
I would like to eventually write a function to send an update when its so far from the last update.
That is good to know. It means that, in the final system, you can put the GPS TX on the Arduino Serial RX pin 0, avoiding a whole bunch of issues with software serial libraries, Timer1, and interrupts.
For now, you can leave the GPS on pins 12 & 13 and use NeoSWSerial. When everything is working (mostly), you can move the GPS TX to the Serial RX pin 0. Uploading a new sketch in that configuration will require either disconnecting the GPS from pin 0 or disconnecting power from the GPS module. I mention that so that you can plan to have a switch inline or a jumper/wire you can disconnect.
Thanks
Glad to help! Now I've got to look at LibAPRS a little more...
Cheers,
/dev
Here are the current requirements I can identify:
Arduino UNO: 50mA
GPS: 70mA
RX/TX LEDs: 20mA
DAC Resistor ladder: ~3mA (assumes R0 is 1K)