About two years back, I developed something similar, using PDF::Reuse to dynamically generate a PDF cover page based on a template and then use pdftk (check PDF::Tk for Perl integration) to prepend it to an existing PDF document.

I tried several modules, including CAM::PDF and PDF::API2 for the merging/inserting pages and although it worked in some cases it was not as reliable as pdtfk. Whether the merging works depends a lot on the individual PDF files, so using these modules could still be a viable solution in your case. In our case the PDFs come from various sources, with different content that we have no control over. But even when using pdftk it still doesn't work with all PDF documents.