You can add bad sectors, you can screw up the TOC use any app...but anyone will be able to rip the files off the CD.
What you really should do is have an exe (protected) and that exe controls all your files, you don't want to use PDF...have to be another format, you really need a programmer for this one...I can only assume this is your IP you want to protect, so maybe it's worth paying someone to do this?
You'll never be able to do anything with PDF format...forget about it!
The only thing you can do with PDF is use their security, which stops average people from editing your files...but they can still rip it off the CD, average users can't edit it or do anything but read it, an't even print if you set the security to no. But this garbage is cracked with many apps available online.
PDF isn't the way for you to go m8.