I had a bricked K3 before I reset it, but Amazon sent me another one. But I did not return my other one, and then I got charged for it in a month's time. U should be able to register it, they simply register it as a second kindle.
So u may not need to strip the DRM off, but have done it to a couple of comics as the hacked PDF application is better for comics.
Back to the topic at hand:
With Calibre u can download meta-data for books, which can include tags or can add the tags yourself, and these can be used by Calibre to create book collections.
I did it a long time ago....but I am sure it would be easier now with tha new updates Calibre has so frequently!