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I have a Classic Nook at 1.5 with about as many books as you have, but I have not had the problems you are describing. Occasionally it doesn't recognize a sideloaded book right away, but usually after just turning it off normally (sleep) and coming back, the book will show up.
However, one thing I do differently is that I seldom use Calibre to send my books over. I usually just use WIndows Explorer and copy the individual epub file from the Calibre library directory. What this does differently is that instead of getting the subdirectory from Calibre, with the epub file, the metadata file, and the cover, all you have on the Nook is the individual epub file. (You do NOT need the other files - you even see the cover image with just the epub file because it contains the cover and the Nook will display it).
You might try doing that. I have NOT had problems sending books over using Calibre and having the whole subdir thing, but since you are having problems you might try the individual epub method and see if that helps.
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