Have you considered using something like XSL:Formatting Objects (XSL:FO)? Basically they're XML documents that are processed and turned into PDFs. Doing string - or better, DOM - replacements within that should be pretty simple. It supports embedding images, links, annotations, etc.
It's not PHP but there are a number of PHP wrappers for it along with ways of using it via exec, etc. Not an ideal but it takes care of the template portion completely. For some more info: http://techportal.inviqa.com/2009/12/16/transforming-xml-with-php-and-xsl/
There's an implementation available as an Apache project - http://xmlgraphics.apache.org/fop/
