A fair bit of an update - most of the payload is built, most of the code is written.
After looking for a suitably sized polystyrene eski/beer cooler for a while & finding almost nothing with the thickness I wanted (25mm+), I gave up and bought a sheet of 50mm polystyrene from a rubber store. I made up a hot wire cutter using some nichrome wire, an old computer power supply and about $10 of wood & steel from my local hardware store, and chopped up what I needed to make a suitably sized box.
The box is now all cut & joined, with recesses cut for the cameras & antenna installed - the transmit antenna is a 1/4 wave whip with a radial ground plane. Camera lenses are separated from the outside world by UV filters you would use on the end of an SLR lens. I'm quite happy with the way it turned out - the GPS module is up top, next to the (backup) SPOT tracker, both pointing to the sky. Most of the weight is down the bottom, with the cameras & batteries, which should keep things the right way up coming down. All the seperate boards are held in a foam core, keeping everything securely in place.
I've got the flight computer logging its data to an SD card, and have been testing it as a regular GPS logger in the car. The Lassen iQ doesn't seem to be the most sensitive of modules, often losing lock between tall buildings and the like, but this won't be an issue in the open sky. My 12mm coin cell holder arrived, meaning I could solder it down and pop in the GPS backup battery - it now takes about 30 seconds to get a GPS lock when the micro is switched on, as opposed to 5-15 minutes without the backup battery.
I've rewritten sections of the GPS code to be more tolerant of failure & also transmit checkum data on transmitted (radio) strings. Still haven't had another go at flashing the arduino's bootloader, for fear of destroying yet another Atmega.
Gary from Air Liquide in Elizabeth organised a good price on Helium for us - $100 less than BOC wanted for the same cylinder size. I'm skipping on the idea of using a regulator designed for filling balloons, as the flow rate is too low. Adjustable flow rate oxygen welding regulators are slightly more expensive, but we won't be waiting 3 hours for the balloon to fill.
My balloons and chute will be ordered soon - not long now!