93 minutes for 80 books is completely wrong. I connected my Aura H2O earlier that has around 1600 books and the "Getting list of books from Device" took 35 seconds. My Glo HD is only taking a few seconds, but I only have about 200 books on it. And those are mostly kepubs from Kobo.
I'm not sure what you mean by 'unselecting the Kobo Touch plugin "Read PDF metadata"'. Do you mean the "Read metadata from files on device" option in the driver config? Unselecting that should only have an affect if there are books on the device that aren't in the calibre library.
The only thing I can think of is if there is a problem with the connection to the device. I would suggest powering the device off and on and rebooting the PC. If it is still slow after that, connect the device without running calibre and try copying some files to it directly. If that is slow, then the problem is not calibre. Or, if you have another PC available, try testing with that to see if it is any different.
The only other thing I can think of is to do a factory reset. If something went wrong with the initial setup and upgrade, this could fix it. And if it doesn't, and none of the above help, it suggests a hardware problem with the device and you should get it replaced.
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