[vrf]

Spent some time, got it working, for me at least.
You have to put your customized font in the Program Files/Sony/Reader/Data/Fonts folder as well. (Similiar to PRS-500 font changing discussed elsewhere.) This then handles the formatting when dumping books on the reader. (The font "wrapping" only works for rendering new font characters... the page layout is still set up for the old font, so you'll be missing some lines of text or will have white space if you only use the wrapper script.)

So...

1. Backup reader books to PC.
2. Format reader memory.
3. Make a backup copy of the fonts in the Sony folder.
4. Copy modified fonts to Sony folder
5. Copy modified fonts to "FONT" folder in Reader memory.
6. Connect Reader to Sony software... upload books... disconnect
7. Unzip Font Wrapping script to SD card.
8. Run script

New fonts now work on books on Reader and books that you add to reader. You'll need those modified fonts on whatever computer you use the Sony software on.

EDIT: BUT You need to reset the device after loading new books on, and then run the script again. This will change once we can flash the Reader with modified fonts.
I'm now running the very lovely Caecilia as my main reading text. Beautifully clear, and just as fast as the native fonts.

I think sturdy slab-serif fonts are the best choice for eink displays. Amazon uses Caecilia for the Kindle, although there are other good ones like Serifa and Calvert.