Is your network back to normal when do try to do the factory restore? If not I'd try putting that back to normal first.
Once you had the root app showing up you didn't need to do the router/non-router root stuff again. At that point you were there - the nook was rooted it was just a matter of working out your connection to it with ADB. So by trying to root again you actually took a step backwards.
I'd say make sure your network is back to normal and then do the factory restore. From there do the root method you did before that seemed to work. Once you have "Don't blink" showing up and the root app starting when you try to go to home put your network back to normal and then focus on getting adb to connect because at that point you ARE rooted and it's just a matter of getting adb to connect (which sometimes takes me a few tries over wireless even when everything is setup perfect.)