I did try to find some additional libraries that might be able to help me but so far I haven't.
Basically what I want to do is edit a PDF programmatically. Since I am already converting the PDF's to SWF I thought I might be able to use something that already existed in SWFTools. The PHP libraries I have found allow me to create a PDF, add things to the PDF but not find and edit/replace something. Or at least I haven't been able to find any references.
How do I modify the text if I embed the fonts?
Using Pdftk, you can do whatever you want with the PDF.
From the pdftk site:
[...]
Uncompress PDF Page Streams for Editing the PDF
Code in a Text Editor
pdftk mydoc.pdf output mydoc.clear.pdf uncompress
[...]
Once you do that, you will be able to edit the text at liberty.
After you're done editting, compress the PDF.
Apologies for going off-topic earlier, I didn't mean it.
Many thanks,
Yousif