Thanks, I was unaware of Lukas Pietsch's work (I'm rather an occasional lilypond user, usually under a lot of time pressure when I finally get to it). I'll go check it out!
I don't particularly mean modern notation in different scalings (the target audience for this particular repertoire is likely to prefer full values, although half might be an option); more different stages of editing: with or without certain ficta rules implemented, for example, or different hybrids among old and modern notation. Part of the project involves organ tablature. I made macros for this for MusixTeX a while ago, and haven't yet got round to investigating lilypond options. At the moment, I've cobbled together a little program that can read **kern input and give functional, if not terribly pretty, lilypond output, but I think I need to figure out far more precisely what I actually need at the end to think constructively about the best way of getting there, if you know what I mean.