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You can also manually add bookmarks:

Table of Contents

After you've arranged your PDF file the way you want it, if you'd like to add a Table of Contents, there's several possible ways to do this. Two are:

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Create a set of pages in an MS Word file that are section headings or starters.  Then, use MS Word's Table of Contents feature to auto-build the Table of Contents, which are links to each of the section pages.  Add this file to your PDF file.  Lastly, move the section pages to their appropriate places in the document, so that the Table of Contents created in Word helps readers navigate to the different parts of your PDF file.  This second option is best when you need to compose opening remarks for each section of your file.  

While viewing your Table of Contents, click the "Edit PDF" Icon on the right.

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

Then, click "Link" on the upper toolbar.

Adobe highlights the spaces where links work in the Table of Contents.  Now that you added a line (or lines) to the Table, the links going to various pages, below the new additions you typed into the Table of Contents, do not properly light up with their corresponding text.  Rearrage them accordingly by clicking and dragging the link spaces.  

Again, click "Link" on the upper toolbar, and choose "Add/Edit Web or Document Link."  

Click and drag with your mouse, to create a new link space.  Follow the steps in the dialog/pop-up boxes to create the link:

• For Link Type use "Invisible Rectangle."
• Link Action should be "Go to a page view."
• Follow Acrobat's instructions to establish the page to which the new link will go.

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 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.  

Create a Table of Contents

Creating PDF Files or Pages using Microsoft Word

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

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.

First, 

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

In this mode Acrobat creates a PDF container that includes files in their original format.  Thus, a .pptx file is still editable (and probably extractable) as .pptx.  When viewed in Acrobat Reader, these files are still in their original format.  This could cause complications for less patient readers, since A-Reader does not automatically preview these files.  Adobe purports to include web pages, but in my test it handled https://www.canisius.edu/academics/office-academic-affairs/academic-institutes-and-centers/center-online-learning-innovation poorly.  

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

https://helpx.adobe.com/support/acrobat.html: Method One

Table of Contents: Method Two