Some things such as fonts are easily done; see
Summary of Modified Fonts which includes naming conventions and where to store fonts.
Library collections would require either managing them via calibre (see
Quick Guide to Shelf Management with calibre 0.9.1 & above (Touch / Glo / Mini /Aura)), or updating the SQL database on the device (see
AutoShelf beta).
Margins you might find some existing patches in the threads I pointed to in the earlier reply.
As far as speed / reflow ... get a dis-assembler and look at the executables.