This method is preferable if you need to compose one or more pages of text at the beginning of each section or chapter in your PDF file.  Since this is so you may as well take advantage of MS Word's navigation feature: Table of Contents.  

In most Word Processors, you can save or export a file in .PDF format.

Here, we'll discuss the simplest method for creating a Navigable PDF file that includes various documents.  There are more complicated methods that potentially provide more and better options, and you can review them by clicking the options below.

MS Word: Write Your Subject Starters 

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 outline or skeleton of your PDF file in Microsoft Word, and add it after you have assembled and arranged all the contents of your PDF file or document.  Since editing files in Acrobat is not efficient, you want to avoid having to make changes to the PDF once the skeleton, or table of contents, is developed and added to the PDF.  If you need to subsequently make lots of changes to the contents, organization, and the table of contents of your PDF document, 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 of your existing PDF, within Acrobat.  

Combine the PDF

First, start by compiling all the files or documents you want in the master PDF file or document.  It is best to add these to a folder, or series of folders, on your hard drive.  This makes it easier to find what you need, and copy it all to backup or long-term storage.  You always want to keep these files separate, since you may need to rebuild them into a new, replacement PDF file later. 

Next, combine them into a PDF file, and arrangement the way you want them.  Here's a tutorial.

(Full Screen)

It is vital that you have everything you need in your combined PDF, and arranged in the correct way, since making changes after you've added your skeleton file will be complicated and inefficient.  

MS Word: the Skeleton File

Next, create a "skeleton file" in Microsoft Word (Google Docs or Pages will work, too) that contains the pages that open each of your sections or chapters ("section-starter pages") and a table of contents.  Here's a tutorial showing how to do that:

(Full screen)

Complete the PDF

Add the skeleton file to your PDF file. Move the section-starter pages into their appropriate places within the document.  The links in the MS Word-built table of contents will be converted into Acrobat's method for handling navigation links, and should remain true to your section-starter pages.  

Here's a tutorial showing how to do that.

(full screen)

On the Organize Pages screen, I add the skeleton file to my combined PDF file.   

It is important that you have your required files in place and properly arranged in the PDF beforehand, so that you can create your section-starting pages, and their corresponding Table of Contents in the proper order in Word.  Having to move or edit these in Acrobat, after you've added the file there, is more complicated and inefficient.  That said, it is not impossible...

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If you elect to add, remove, or just move sections around, that's simply a matter of using the tools fond in the Organize Pages screen:Image Removed, and the previous instructions.

Image Added

But editing the Table of Contents is another matter.  While viewing your Table of Contents, click the "Edit PDF" Icon on the right.

Image Added

This will create a text box boxes around your Table of Contents list.  You can click inside, and type in the new item, just as you would in Word.  

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As you can see there's a lot of steps and some careful mouse-work to edit the Table of Contents in Adobe.  For this reason, try to assemble everything you need, and build your Table of Contents and Section Pages in MS Word, first.  If you have extensive edits to make to a Portfolio, consider recompiling it a new PDF file.  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

...

Create a Table of Contents

https://www.youtube.com/embed/-yUS89t3Alg

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.  

PDF Portfolio feature in Acrobat

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In short, this is too complicated for most who might read a PDF portfolio, and would result in an untenable support burden for COLI.  

Organize Documents

Now that your documents are installed, 

Rearranging Files

Rotating Pages

Adding Page Numbers to a PDF

Is it possible to have Acrobat create the page numbers, and then after that, add the TOC?  So that you get the entire document exactly the way you want it, and then as a last step add the TOC?  

Creating a Table of Contents for a PDF Document

Create the Table of Contents using Microsoft Word

Creating a Clickable Table of Contents using Adobe Acrobat

Resources

Resources

Adobe Acrobat's User Guide and Tutorials: https://helpx.adobe.com/support/acrobat.html

Transcript for the above video tutorials: https://docs.google.com/document/d/1iQRD8_Ih8omkBHYgQG6krhjZV4DfdTJHnssogY7frEM/edit?usp=sharing