I have the same problem. I tried htmldoc and unfortunately, while it did the job, it created a lot of weird characters (A with a hat) here and there throughout the document.
I tried to put some htmls together in the same folder, and then use an html file that I created as stated in the calibre website, and tried to convert to pdf using calibre, but I got an unopenable pdf.
I'm now thinking I could probably just copy and past contents of each page onto openoffice and create a pdf from there, although that's a pretty inefficient solution as I have other books that are like this.
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