I'm late to this thread, and I might be missing some crucial aspect of the problem, but if you just want to integrate lilypond scores and fragments into a LaTeX document, and you're able to choose to use Luatex, the lyluatex and lilyglyphs packages work beautifully with the latest Lilypond versions.
I can supply a shortish example if you wish, but I'd rather do that off-list (i) in case it is not helpful to you, and (ii) to avoid cluttering the lists. -- Graham
