Very interesting! I recently did a simple conversion of the Lini v2 code from ASM to C although I am not sure if James put it up on the PICList page yet. My conversion was done quite quickly and doesn't have the PWM range so no 18th steps.

Why use EEPROM for the tables?

Good call on dropping the ability to change step modes when running, nobody uses that feature anyway.

I'm not sure about the quadrature input, it should be pretty fast using standard step signal anyway if you are using a 16MHz or 20MHz xtal.

Do you have a link to a text file for your source code? Many people don't like downloading a ZIP because of potential viruses etc, and the source code should only be tiny anyway so it doesn't need ZIP compression.