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Okay, so I opened the PDF in Adobe Acrobat zoomed to 4% (this is when the cover shows at the correct size), copied the page, pasted it into MSPAINT and it was the correct size still. Then I simply pasted (it's already in the clipboard so didn't even have to copy from MSPaint) it back into the PDF file between the cover (huge original one) and the normals size first page of text. I then deleted the huge original cover page, saved the PDF (it did add a little size to the file, probably because I messed with it's chi, but whatever. Then I went to Calibre and it was able to extract the cover like normal, so the problem is solved it would seem. Maybe it'll help someone else too. Although, I still don't have an automatic way of finding the PDFs with too big of a cover page that will cause this problem or corrupted PDFs that will just not allow opening and therefore extraction of the cover.
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