Hi Chris.
I am one of the Moderators on the forums at MyBeBook.com. Please feel free to register and make use of the wealth of information and experience we have over there.
To answer a couple of your issues. First, the firmware on the site is later than the one you have and I recommend you update. PDF and Epub handling has been much improved and your large PDF's should work better.
Second, the PDF's at Archive.org will always be a problem for any reader because they are basically photo scans of the original works so there is no text or formatting to work with. OCR scans are much better but you have probably realised this by now. DJVU works very well, so I am told, and there are several different firmwares available, one of which really excels with the format. You will find them discussed quite heavily in this subforum and they are quite safe to try. You can't brick a BeBook One with a firmware update.
As I said, come over to the BeBook forums and let us help you.
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