The reason touching the screen on the Glo went to the home screen is because the processing had finished. There might have been an error as well and one or more of the books weren't processed properly. But, I have seen this very occasionally and it mainly seems OK.
As to the Touch, processing a lot of books takes time. 30% of 5000 books after 90 minutes sounds about right. Slowing down as it goes also sounds right. The Touch will be slower than the Glo as it has a slower CPU and, from memory, less RAM. I've never tried to load that many books in single batch, so I don't really know how long it will take. About the only thing you can do is plug it into power and wait.
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