Can my consultant provided PDF files be included in my project manual?

Yes.  Use the Insert Documents > Import Docs from File System menu pick.  The Importer will automatically setup the Numbers, Names, and Division Folders based on the filename of the PDF(s) which you may edit in Step #3 of the Importer if needed.  Be sure to right click in the project tree to View the Item Info and uncheck Exclude This Document From The Table of Contents if you want the TOC to automatically include the PDF(s) and page counts for you.