How to upload pdf files and link to them?
I think the solution could be IMCE module which allows you to upload file/images... through CKeditor interface.


  Features
  
  
  Basic file operations: upload, delete
  Image(jpg, png, gif) operations: resize, create thumbnails, preview
  Support for private file system
  Configurable limits for user roles: file size per upload, directory quota, file extensions, and image dimensions
  Personal or shared folders for users
  Permissions per directory
  Ftp-like directory navigation
  File sorting by name, size, dimensions, date
  Tabbed interface for file operations
  Keyboard shortcuts(up, down, insert(or enter), delete, home, end, ctrl+A, R(esize), T(humbnails), U(pload)).
  Built-in support for inline image/file insertion into textareas
  Multiple file selection(using ctrl or shift)
  Ajax file operations
  Themable layout using tpl files