Polishing up a score

[Tim Knigge]

Hello,
Over the last couple weeks I have been entering the Art of the Fugue in
lilypond format as a contribution to the Mutopia project using lilypond
1.4.7.
All parts have been entered and I am now looking at polishing up the
resulting score as there are some things with which I
am not completely happy. Maybe someone can give me a few pointers on to how
to solve the following problems:
- Sometimes note collisions are not handled very nice (especially it seems
when a 1/1 note is involved). To see an example, download
 contrapunctus 7 from the Mutopia project. In bar 60 two voices collide on
d in the lower staff (a 1/4 and a 1/1 note). Obviously I would want
  the output to look similar to bar 52, where a collision on f'' is handled
elegantly.
- Also occasionally rests (partly) collide with notes although the
documentation suggest that lilypond should automatically move the rests
'out of
  the way'. To see an example download contrapunctus 9 from Mutopia and
look e.g. at bars 22 and 25. I see no reason for the 1/1 rest to be
  so close to the 1/16 g and 1/2 e respectively. It would look much better
had the rest been positioned one staff line below where it is right now.
I know I can prevent some of these problems by introducing additional
staffs, but I would like to keep it on just two staffs.
any help is greatly appreciated
regards,
Tim Knigge