"having Perl scripts generate all those pages would be messy anyway, let alone trying to incorporate jQuery as well."

Yeah, that's why I use HTML::Template, it's pretty much the same as having a standard HTML file with the exception that you can populate (via non HTML, HTML::Template specific tags) the HTML/JavaScript/jQuery/css from from Perl, in my case, our Oracle databases. Perhaps overkill for what you are working on, but I'd suggest looking at a templating system, see Framework, Templating, and Content Management Systems from the tutorials section for further reading.

Best of luck

Martin