This is the Chilly Hilly version with the Triangle Bag & Rear Boot bag. Easy to find these items at most bike-handy stores. The Triangle bag came with my kit from Ebikes.CA, and the boot bag came from REI. I used high-density closed-cell foam for protection. I could fit 6 to 8 batteries in the Triangle, and up to 14 in the boot bag.
For my first cross-country road trip in 2010, I moved all the batteries to the panniers. A simple aluminum shield was constructed to retain the shape and prevent crushing. See below...
Though it could hold up to 12 per side, I used 9 for each pannier so as to have room for food.
Then I created a large capacity battery bag assembly using two camelback bags sewn together. It went through a few permutations until I found a configuration that prevented it from getting wet. Each side holds 9 batteries.
Original w/ boot bag strapped on board.
Started adding fairing bits of shielding...
Full-wrap of HDPE, though still getting wet.
The pre-2WD version has a double-wrap around the bag: Tough marine vinyl inner wrap is water-repellant, with a high-contrast wind-slippery HDPE outer wrap which makes it easy to wipe down and keep clean.
Inside view: The front is to the left. Though it could hold more, I settled on 15 per side.
In addition, I have a saddle bag made from two Timbuk2 Front bike bags that lays over the top of the triangle assembly; it's on the right and each side holds 6 batteries. The left packaging is for the trailer and allowed me to quickly remove it for balancing when required. The center packaging is for the panniers.
Altogether – it looked like this for the 2011 road trip:
I continue to scheme up ideas with necessity being the mother of invention. Lots of ways to skin the kitty. Though I still pine for a really nice hard-covered solution as the ultimate protection against the unwanted collision