> and a 3V to 5V step-up converter
You may want to step it up to 3.3V only for the main power supply and do a little surgery on the Pi to feed it directly to its 3.3V 'rail', foregoing the 5V->3.3V linear regulator. (I'm just saying this from reading the given page, I haven't done this myself, so YMMV.)
http://www.bitwizard.nl/wiki/index.php?title=Reducing_power_...
BTW it's not clear to me whether the Pi or the Beaglebone Black use less power [when idle]. The latter would provide more CPU power, which would make it more interesting for a general purpose solar computer.
PS. I was thinking about the B+ when writing the above (stupid me, should actually read the article before posting). The A+ likely has lower power consumption than the Beaglebone (but also only 256 MB RAM, which is really going to be limiting for many tasks). Also, perhaps they have replaced the 5V->3.3V linear regulator with a step-down regulator which would be more efficient (still, doing only one transformation instead of two would give you a bit lower losses).