Welcome,
There have a been a number of successful high altitude balloon projects using CHDK, you can probably find some useful information searching the forum. Searching "balloon" should get some useful results.
I especially recommend Francesco Bonomi's work
http://www.francescobonomi.it/photo-balloon you can find some more information by searching his forum user name "fbonomi"
There are also numerous discussions of turning the screen off for power saving.
and it appears that the autofocus mechanism is staying active despite using the "Override Subject Distance" feature from the "Extra Photo Operations" menu
Subject distance override doesn't disable Canon AF, it just forces the focus to the desired value after the canon AF process is complete (if it works, this is a notoriously buggy feature...) I'd suggest using the built in focus at infinity mode if your camera supports it, or perhaps canon manual focus (although this may actually consume more power than AF)
If you do leave AF on, you might want to try different canon AF modes. I'd suggest leaving AIAF, face detect etc off and just going for a fixed center AF box.
