Paul,

You have a difficult task before you.  Identifying passerines down to
species level would require extensive use of a very complete comparative
collection.  Osteological guides are useful in helping to narrow the field,
but for making specific identifications it is essential to have an avian
osteological collection to make comparisons.  I am a zooarchaeologist and
having identified bird bones from archaeological sites, I think it will be
very hard to identify passerines down to the species level since passerines
is a very large order and these are small birds with very similar
skeletons.  It may only be possible to identify them to the level of genus
or even family.  I am not sure how many distinctive features are present on
passerine skulls.  These skulls are from owl pellets you said?  Do they
contain other intact bones?  If you have a variety of elements to look at,
perhaps you can do even better.

As for references, I would suggest:

Cohen and Serjeantson (1996).  A Manual for the Identification of Bird
Bones from Archaeological Sites.  London:  Archetype Publications, Ltd.

Gilbert, Martin, and Savage (1985).  Avian osteology.  Arizona:  B. Miles
Gilbert, Publisher.

Harrison, C.J.O. (1982).  An Atlas of the Birds of the Western Palaearctic.
 London:  Collins.

Perhaps you might want to put your inquiry out on ARCH-l where you might
catch the eye of other zooarchaeologists who have done similar
identifications.  It is a difficult task, but not impossible!  I hope some
of this information will be helpful.

Best of luck,
Andrea Shapiro