I have opened a new thread as the problems grew a little too complex.
http://lists.gnu.org/archive/html/lilypond-user/2009-01/msg00788.html
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the solution is also
described here:
http://lilypond.org/doc/v2.12/Documentation/user/lilypond-program/Setup-for-MacOS-X#Setup-for-MacOS-X
Have fun!
Elmar Koch (with special thanks to Kieren MacMillan for his contribution)
#!/bin/tcsh
# Set the path to lilypond-book
set path = ($path
/Appli