You could get a precompiled ARM build of calibre using ArchLinuxArm instead of debian.
As for automating calibre, ebook-convert (cli interface for conversion) accepts *.recipe as input for scripted news downloads. Just check the internal name of the news recipe, see:
https://github.com/kovidgoyal/calibr...master/recipes
But the main problem is that calibre uses a lot of memory to convert books. A mere 256MB won't begin to cover your needs.