Massorah and PDFs
Michael is right - there is no way to convert the PDF to HTML, unless you use OCR software. But that will work badly with the small text sizes and Hebrew, so it wil be easier to just type the text in. Converters that go from PDF to HTML only work if the PDF has embedded text, which is not the case here.
I developed the sample Ginsburg module, so I can do all the technical/difficult bits involved in actually creating the Module file. It just needs volunteers to type in the text as far as possible. I could do any tidy ups, and work involved in getting the text into exactly the right HTML format, if people found that difficult. So potentially, volunteers just need to enter the text. It would work in a similar way to Michael's suggestion.
This would be a major undertaking, but along the way you would learn a truly immense amount about the Massorah, and how it worked across the 70 or so manuscripts that Ginsburg collated. There is no way you will learn that information any other way. Even if we had to stop part way through due to lack of time or volunteers, the progress up until that point would still be beneficial.