Yes FPDF is to generate PDF files, you can find PHP scripts to read DOC, XLS files and then you need to write conversion script to convert to PDF, It is going to be lot of coding. I havent seen any free PHP libraries which do this.
You may able to install OpenOffice and use COM objects to automate something similar to what you trying to do. But these are very server intensive work, may easily bring down server if you handling lot of files
OpenOffice PHP COM Documentation