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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.  

Combining PDF Files 

Combining files into a single PDF file

What file types will Adobe include in a .pdf? 

https://helpx.adobe.com/acrobat/how-to/combine-files-into-pdf.html?playlist=/services/playlist.helpx/products:SG_ACROBAT_PK~12/learn-path:get-started/set-header:ccx-designer/playlist:basictraining/en_us.json&ref=helpx.adobe.com

Adding files to an existing PDF File. 

Adding Page Numbers to a PDF

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