Hello
I can create a script for you to convert the html files to pdfs, I could create a shell script with a wrapper that can recursively go through a folder and turn any html files into pdfs.
If you would like to send through some additional info on which version OSX you are running and the folder structure you are currently using, we can confirm and go from there.
Thank you.
Edit: Just a quick follow up, the additional link you provided to scott gamers github project has not been updated since before Mountain Lion (OSX 10.8) and he notes he will not be providing any further updates to it, so I would not recommend using that method. Also it has been designed to download URLs and convert to PDF, where as, if I understand your project correctly, you are wanting to convert html files that you have already downloaded, into PDF files?
I can build a script that will utilise the core OSX features to do the job.