Acrobat or QaurkXpress for what I need to do

As you already have the MS Word files all you need is a means to either:
--| create 1 PDF from many Word files directly
or
--| create PDF files from the Word files & then combine many into one.Acrobat Standard and Professional provide this (the Combine > Merge Files int a Single PDF).
This can be done directly with the MS Word files selected or with PDF output from MS Word files.
(Many MS Word files to 1 PDF or many PDF files to 1 PDF)

Some comments/observations:
It is possible to output each Word file to a PDF using the Microsoft Save As to PDF or XPS (Office 2007).
But, you still must combine PDFs - No help with that from this feature.

If you use QuarkXpress, you can use Quark's feature to output PDF (after you bring the Word files into QuarkXpress & perform any needed cleanup).
But, you already have your content mastered in MS Word - why duplicate this in another authoring application?

If you use Acrobat Standard or Professional, upon its install you will have the Adobe PDFMaker & Distiller.
These permit output of robust PDFs from MS Word.

Comparing the retail cost of QuarkXpress and Acrobat Standard or Professional and taking into consideration
what you have identified as the task it would seem that Acrobat is clear choice.

With that said, you may want to web search for free / shareware / low cost PDF related routines.
(keeps the cost down - but the quality/usability for "PDF" things other than display of page content can be problematic with some)
There are third-party programs that can do focused tasks well. One or more of these may be sufficient to your task.

Be well...

Thank you SO much--very thorough answer and I appreciate it. I think my concern was making sure that Adobe could handle a 1000+ page .pdf document (that's the only reason I would have gone to something like QuarkExpress or InDesign, etc.). But it sounds like that's not a problem with Adobe Acrobat, so seems like the clear choice. Thanks again!

Handling a large page count PDF is less a function of Adobe Reader / Acrobat and more a function
of the caliber of computer being used by you or your users. Large page count, of anything, is a load
on the "motor" (the computer).

Keep in mind that, if the 1 or 2 page Word files are "heavy" with image content, processing
many at one time (by [i]any[/i] application) can be a significant load on the local machine's resources.
Particularly if integrated graphics vice dedicated graphics card (with some 'umph' for onboard RAM) is used.

Another consideration, for any repeatative processing of many files for anything,
is the population of processes running on the local machine.
Often, more chafe than wheat with this; so, you may want to consider turning off some of them.

Also, consider doing the following:
--| Use Fast Web View for the deployed PDF(s)
--| If PDF is on a web server, be sure the server is configured to page-serve
--| Add cataloged index - use the PDF's Document Properties > Advanced tab to "mount" the PDX file when the PDF is opened.
This will enable use of Search (more potent than "Find").
--| Incorporate PDF Bookmarks & configure PDF to display bookmarks & page view
(PDF's Document Properties > Initial View tab)
Use Adobe PDFMaker to designate Word Headings &/or Styles that are to be made PDF Bookmarks.
Finding what you want/need in a PDF of some few hundred pages, without PDF Bookmarks, is a bloody pain.
A PDF of 1000+ pages really must have at least one PDF Bookmark for the start of each unique grouping of document content.

Make it "Easier to use than falling off a log in the water."; then its Chivas time .Be well...

Wow, you are amazing--thank you!

Do you by any chance do any contract work? Might be best to have you start this project for us so that everything is set up correctly and then we can keep adding to it as time goes on.

Let me know, please, if you'd be interested in anything like this.

Thanks so much!