Hello,
We have an extremely high level of experience interacting with PDF files. We've developed invoice applications (PDF based), PDF parsing libraries, html / PDF conversions, and many many more. We have more than 15 years of PHP experience.
We would plan this project in three stages: First we would analyse the website technology and decide what to use (the key factors are the possibility to run a utility application on the server, the amount of RAM memory we have at our disposal, how many requests per second must this library resolve, what kind of framework - if any - you're already using... In a word, analyse the environment and make a decision about implementing the project). Second, create a PHP library that accepts the PDF file and the required parameters, make the changes and returns the modified PDF file or the same one, with all modifications requested . Lastly, we'll integrate this library in your web site, most probably by hooking into a user event with Javascript.
All the code we deliver includes phpunit testing with code coverage. The code is throughly commented in order to make the maintenance and / or further development a breeze.
Please do not hesitate to contact us for more details.