...

Is it possible to enact this plan?  Create a skeletal document using Microsoft Word, that includes a clickable TOC.  The TOC only highlights pages where the faculty member will provide some sort of introductory page.  So when you assemble the final portfolio, you put the scanned or otherwise collected documents in among these introductory pages, such that the clickable TOC is entirely built in Word, rather than having to fuss with it in Adobe.  It's doable, and editable in Acrobat, because it appears that Acrobat converts the .docx internal links to PDF Document Links.  But, two caveats:

• Don't add page numbers in Word.  Once you add the other content in between, they need to be updated anyway.
• if you need to edit the resulting PDF it's a pain, because you would need to shift the links down, and create new ones in the TOC, which is complicated and not for the impatient.  

Combining PDF Files 

When combining files into a PDF file, it's important to remember that Acrobat is not a content creation tool, so much as a document publishing tool.  The distinction is important, because you wish to create the final outline or skeleton of your PDF file in Microsoft Word, and add it to Adobe Acrobat, together with PDF files.  Since editing files in Acrobat is not efficient, you want to avoid having to make changes to the PDF once it's assembled.  If changes to the contents, organization, and the Table of Contents itself are extensive, you may find it's easier just to recompile your files into another PDF, rather than attempt to make changes to the Table of Contents within Acrobat.  

Combining files into a single PDF file

...