Your discussion points out a couple of limitations of Barnes and Noble and the Nook Color.
Your first problem was with product support. B&N are book sellers and do not seem to yet have the staff and systems to handle support issues related to the reader hardware and software. They are in the middle of trying to transition their business to electronic media while their revenue stream from their current core products sucks. Even with the best of intentions, it's hard to ramp up training and business systems while Amazon is eating your lunch on your core business.
Fortunately, there are several online communities, like this one, with people who are willing and able to help you work through technical issues like these. Did you try to get help there? Some of the SD card problems could have been caused by formatting or partitioning issues.
Second, you seem to be an ebook "power user" with needs a bit different from what I would consider normal. This does not mean they're unreasonable. The Nook Color is designed to be an ebook
reader and incorporates the concept of a book shelf which represents a small to medium collection of books. It looks like what you want is an "elibrary" and that is probably outside the specs that the Nook Color was designed for.
Please keep in mind that B&N's primary purpose for the Nook Color is to help them sell you ebooks. I doubt that they make much, if anything, on selling the hardware. Just for curiosity, how many of your 3000 ebooks were purchased from B&N?
It could be that your best option today is to use Calibre to handle the library functions and to copy books, or small collections of them, to a reader like the Nook Color when you are ready to read them. It certainly should do fine for a month's worth of reading material.
As an ebook READER, the Nook Color seems like a good deal to me. It's clearly not as good as a library management system. If someone else knows of a single product that does both well for a reasonable price, I hope they'll mention it here.
To be honest, the Nook Color doesn't doesn't do everything I want either. It just seems to be the best solution for my needs at this time. After a couple of weeks of research, I'll finally go buy one today.