Michael, kudos for the links; very cool.
You know, it's almost more interesting to see a 2-color approach because afterall, we're so used to seeing beautiful, 3-color reproductions that nearly mimick reality. It's more interesting/profound to see something that's slightly different from reality. I'm on your 2-color bandwagon!
Hey, check out this book and go to Chapter 5. It's the Friedman book I've been alluding to. He basically outlines all approaches that have been taken for color-separation cameras.
You're sure to find some new, novel idea that perhaps hadn't occured to you before and might make your task easier. It's what I would describe as "very thorough".
As for the two-color requirements, are you still searching for the appropriate filters to do it? I'm sure this information is in some book somewhere, I'll try to do some searching.