Thanks for the response, Kovid!
A little googling brought me the solution, for the people looking for one.
If you have the Pro edition of Adobe Acrobat, you can OCR the text, even after it has been scanned. It takes a little time (since it analyzes every page from top to bottom) but it's definitely worth it. After the process, save it, re-put it into calibre, convert it (now the conversion doesn't take long at all), the file is way smaller (just 3mb) and it works perfectly on the kindle.
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