It's great that you tried softrooting (twice) - apps are in the early stages and free, but I'm sure that the apps will improve...
I may be able to address a few of your issues:
"Problem 1: The softroot swaps the order of drives."
This doesn't happen on a Mac, and for Windows, there's a pretty straightforward drive letter re-assignment that seems to work (
here).
"Problem 2: Calibre has updated the online catalog file to better meet standards."
Sorry - I haven't experienced this, but hacking is what Nookdevs is about - that's half the fun!
"Problem 3: The Nookdevs software responsibly accesses only WiFi (not the B&N Network) but has some sort of trouble staying connected."
Nookdevs WiFi disconnects when the WiFi isn't being used - I haven't had disconnects when accessing the B&N store, or the Web. The "stay connected" helper app is when you access your Nook via VNC as the underlying VNC server doesn't keep the WiFi connected.
"Bleh 1: Other than the merged libraires, the additional apps were not particularly handy for me."
I know what you mean, although I like the PDF viewer for rotation and zoom. I'm also having fun with Android sources and am currently modifying an Andriod z-machine for playing interactive fiction (Twisty).
"Bleh 2: Pandora Radio...is still a bit of a hack"
Agreed.
Maybe it work be worthwhile to try again in a couple of months to see how things have progressed. With so many Andriod apps, it shouldn't be too long before a significant number are modified to run on the Nook.