...and here it is! Stock Reader with custom fonts in the select-a-font-thingy (and the italic/bold-fix, of course).
Fonts are specified in /sdcard/fonts/fonts.xml, and if that file is not found or cannot be read it falls back to the stock fonts.
"Screenshots" attached, with exaggerated fonts to make it clear that it works (the reason "Bold italicized text" is not italicized in one of the images is that I had no bold-italic file for that font, so i set the bold file as bold-italic).
As you can see, the "Selected Font Type" thingy does not show the custom font name for now; it consists of a bunch of hard coded button resources and so requires a bit of extra work to replace.
File:
http://morkl.se/reader/readermod_v2.zip (contains loose apk as well as installer for non-rooted devices; and fonts folder with sample settings)