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.
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.
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:
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.
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...
Editing Your Table of Contents in Adobe Acrobat
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, and the previous instructions.
But editing the Table of Contents is another matter. While viewing your Table of Contents, click the "Edit PDF" Icon on the right.
This will create text boxes 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.
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.
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