Converting HTML to PDF using convert utility in Mac OS X
Have a look at wkhtmltopdf— a command-line utility that uses the WebKit rendering engine to produce PDFs from HTML. I've found that it produces a nicer result. You shouldn't have any trouble integrating it with your current script.
Have you considered writing an AppleScript script to open each HTML file in a scriptable web browser (like Safari) and then using the browser's standard print command to print to a PDF file?