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Don't convert it. As has been noted before multiple times and in the Calibre manual, PDF is the worst format to convert from.
Because archive.org is currently down, the file can't be accessed to view it. However, from what you're describing, it sounds like a heavily image-based document. If so, that's your problem. All it does it take the pages and convert them to images in the ebook.
If you want an actual, proper ebook, you would have to find one already formatted as such, or do a bunch of extra work to get it the way you want.
Otherwise, your best bet is to just keep it as PDF.
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