Don't know if this is an option, but it would work very similar to Zend's pdf library, but you don't need to load a bunch of extra code (the zend framework). It just extends FPDF.
http://www.setasign.de/products/pdf-php-solutions/fpdi/
Here you can basically do the same thing. Load the PDF, write over top of it, and then save to a new PDF. In FPDI you basically insert the PDF as an image so you can put whatever you want over it.
But again, this uses FPDF, so if you don't want to use that, then it won't work.