Check out FPDF (with FPDI):
http://www.setasign.de/products/pdf-php-solutions/fpdi/
These will let you open an pdf and add content to it in PHP. I'm guessing you can also use their functionality to search through the existing content for the values you need.
Another possible library is TCPDF: https://tcpdf.org/
Update to add a more modern library: PDF Parser