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I bought the N2A card for mine, so I don't have any answers on what may or may not be working with your root, and haven't entirely worked out how to get rid of the unnecessary cell phone stuff myself.
As far as reader apps go, I found that Mantano was the easiest for me to use as far as library organization goes. A lot of the other apps required me to browse for files or put them all in a specific folder first, and then ignored any metadata I'd set in Calibre. Mantano doesn't care where the files are, it syncs from everywhere on the device, AND it recognizes tags and metadata from Calibre. No shelves as far as I can tell, just a basic searchable list like the stock Nook reader, but the tags make for fantastic organization.
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