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Processing new books became dramatically slower in the current firmware 3.2.0, the previous version was more than 10 times faster on my Glo. If its not fixed in the next version you might consider going back to version 3.1.1.
In any case it is probably a good idea to just load a few books at first until you sort out how things work. There are a lot of options to improve the appearance and functionality of the books that need to be selected before sideloading them.
For example the wasted space at the bottom of the page in epubs is caused mainly by the orphans/widows stylesheet settings. This can be fixed by using an option in Calibre to modify the book's stylesheet as it is sideloaded. Better to discover that option (and many others) before you load your entire library.
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