So... keep in mind this is the type of thing that can easily go wrong if you don't know what you are doing.
(No kidding, you are overwriting the operating system.)
The official update .bin file can be extracted using
KindleTool, and contains a "rootfs.img" which can be used to overwrite the root partition (/dev/mmcblk0p1).
You might want to flash the kernel while you are at it too.
It's in the unpacked update as well.
...
Once you've flashed a new firmware, it is no different from applying an official firmware update. Namely, you need to reapply all hacks, although the jailbreak itself should still be bridged (assuming you did the right thing and left /var/local alone).
...
But of course this only matters in terms of your objectives.
Font size -- have you seen the non-jailbreak "FONT_RAMP" file tweak?
Hyphenation -- what hyphenation hack?
Margins -- if you are referring to kaznelson's modified jars, sure. Although maybe it wouldn't be a bad idea to update that hack instead.
It comes with directions IIRC.