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In response to Item 2, no, you can't swap out the images in buried folder locations for the cover thumbnails like you can on the Sony. I also do not think it is possible to change the B&N book covers since it is syncing those books with the B&N servers.
Also, there may be an issue with how covers are displayed for DRM versus non-DRM'ed books. With my Nook Color, which has similar firmware, the non-DRM'ed books mostly have covers. If not, then I do a calibre conversion as noted in the previous posts. However, the DRM'ed books (like ones I purchased from the Sony or Kobo bookstores) show a generic icon rather than the cover art. Perhaps somebody can clarify if the Nook Touch has this same issue.
Item 3. The pagination will be similar to your Sony. That's the nature of EPUB's. It does not dynamically repaginate for font sizes. On the other hand, if you were to go to Page 213 on the Nook Touch, then you will see the same text as Page 213 on your Sony.
FYI - If you have a really large library of non-B&N books, then you will probably need to store them on SD card rather than the Touch main memory. The Touch only has 250MB of its internal memory allocated to side-loaded books; the rest is reserved for B&N content.
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