I chose 3/8" rod becasue i wasn't sure what the strength of the rods would be. After completing the project I can say they are overkill.

full parts list for bags as seen:
2x 36" 3/8" threaded rods (24" rods would work)
4x 3/8" acorn nuts
16x 1.25"x3/8" washers (overkill, smaller would have been fine)
16x 3/8" nuts
2x bungee cord
2x large wall mounting hook
8x large zip tie
2x marine battery box (series 27 i think?)
2ft 3/8" ID black tubing
2x reflectors (optional)

Tools Required:
Drill and 3/8" bit
wrench
torch or lighter (to seal ends of bungee)
small vice grips and adjustable crescent wrench (optional, to tighten zip ties)

There are a few details of construction that you can't see very easily in the pictures so I'll list them for anyone wanting to build this or use ideas from this to build something different:

• the hooks that hold the bungees to the bike are standard wall mounting hooks sans the nails.
• the bungees were cut and held to a flame to seal the ends and prevent fraying.
• zip ties fastening the ends of the bungees were pulled super-tight using vice grips to pull the ends while an adjustable crescent wrench provided resistance. I believe the zip ties are an inferior way to secure the ends and if you have the recources available i would recomend using pinched metal C rings. I used 2 zip ties per end as a fail-safe but i know the plastic ties will wear out and need replacing eventually.
• the bungees need to be a lot shorter than you'd think to get good resistance and keep the boxes from chattering against the rack as you go over bumps.
• acorn nuts with a bit of locktight 'finish out' the ends of the threaded rods. These aren't required but they look nice and i think the acorn nuts only cost $0.20 a piece USD.
• 24" threaded rods should be fine, i bought 36" rods becasue I knew the numbers would be close but after measuring the final rods they are almost right at 24". There may be multiple rack widths so YMMV.
• I used 1.25" washers on both sides of the plastic each at location a rod went through. I don't think you need washers this big and using smaller washers would allow the rods to be placed further toward the ends for the boxes.
• The threaded rod will evenutally rust. I have considered painting, covering with split tubing (like wire loom) or other options to prevent rust but I have not done anything yet. I wanted to cover the entire rods with tubing (except where the nuts/washers were) but it prooved to be to much work trying to get tubing on the rod sections inside each box.
• Wal-Mart automotive section was the cheapest place i found battery boxes at. they were about $1 a piece less than Advanced Auto, Pep Boys, Oreily Auto, NAPA, etc.
• I added some orange reflectors i picked up at walmart to the back for a little extra visibility.
• If heal clearance is an issue becasue of the geometry of your bike, you could put the rods through the boxes a few inches down from where I have mine. This will raise the boxes a bit and give a little extra clearance.

If anyone does build one of these or something similar I'd love to see pictures. I'm working on another mounting system for some mini-trashcans using cable clamps as tiny U bolts but it'll be a while before i have pics to show for my work. Have fun!