I went though this last week and really ended up nowhere
I've been told that the problem was that I was running 1.0.1 upgraded nook. I don't know for sure, but I did get android installed, and "sort of working". But I was unable to switch apps or get back to the nook reader without reboots.
I ended up doing my best at a factory reset. First off by deregistering from the settings menu and then by holding the 2 page buttons after a power off. I'm still not convinced that all the android stuff is gone. If the little droid man pops up again I'll do the 8 restart routine.
I think that rooting is worthwhile, but I'm going to wait for a better version