I'm really enthusiastic that this particular idea of epub tweaking found that much positive resonance - really no joking here.
Tox: while you work on manipulation of the font files you should consider auto-renaming them: both filename & the font name stored inside the font file. AFAIR It's often required even in licences of free fonts when they are changed. While it's relatively meaningless for personal uses it's crucial as soon as your tool matures to become a part of the toolchain used by professional producers. (and aren't more optimized professional books a goal we all wish for?)