This is what I do at Wikibooks:
I create a special wiki page that is the "print version" of the entire book in a single wiki page, for example:
As you can see, the "edit view" of the print version of a book looks something like this:
= Introduction =
{{:Robotics/Introduction}}
= Contributors =
{{:Robotics/Contributors}}
= Stepper Motors =
{{:Robotics/Stepper Motors}}
= Navigation =
{{:Robotics/Navigation}}
= Resources =
{{:Robotics/Resources}}
= References =
{{:Robotics/References}}
Then I go to each and every wiki-page of the book,
hunting for the magic words "<references />" and "{{reflist}}"
and make sure each one (if there is one on the page) is inside "noinclude" tags, like this:
"<noinclude>{{reflist}}</noinclude>".
Except for the very last "References" page of the book, which has a "{{reflist}}", but it does not have any "noinclude" tags.
Then when I look at the "normal view" of the print version of the book ( http://en.wikibooks.org/wiki/Robotics/Print_version ),
those references are not included at the end of each page (because of the "noinclude" tags),
but only in one giant list of references at the very end of the book.
I suppose you could make a "print version without references" page identical to the "print version" page, except delete the two lines
= References =
{{:Robotics/References}}
so that "print version without references" page never includes the magic words "<references />" and "{{reflist}}" unless they are hidden by the "noinclude" tags.
Then you could produce the PDF file from that one big "print version without references" page.
More details: http://en.wikibooks.org/wiki/Help:Print_versions
p.s.: I'm one of the people who often thinks articles at Wikipedia and elsewhere don't have enough sources. Please consider yourself lucky that you have so many references and sources.