Hey guys,
I was having the same problem as a lot of you: despite everything else seeming restored, my internal storage wasn't accessible over USB. Under device info, the nook also told me the storage was "not available".
Well I found the problem! I don't know exactly how it got there, but there was a small (~1mb) unformatted area on the disk. Somehow this was stopping the nook from recognizing internal storage (i.e., the NOOK partition).
The trick is, these little areas don't show up on any of the windows partition software I'd been using (EaseUS, MiniTool)! They do however show up on the Linux tool Gparted.
If you're a linux noob like me, you can get Gparted running pretty quickly by following these instructions: h t t p :// gparted.org/liveusb . p h p (without spaces). All you need is a usb drive to fit the .iso (173mb). Once you have the tool running, you'll need your nook attached with Noogie running off the sd card to access the partition table. Assuming your problem is the same, you can just modify the size of one of the last three partitions (NOOK, cache, userdata) to absorb the unused space. Voila! While you're at it you can give yourself some more space in the side loading partition (NOOK) if you'd like. I got userdata and cache down to 100mb apiece and now I have 1gb for side loading!
Hopefully this makes sense. I just spent 4 days trying everything possible to get this working again and I don't want anyone else stuck on the same problem, so let me know if you need more detail.