The Book Code

This is a puzzle I put together using books that I own. You have to solve it to learn my secret. :^P
Interesting! One of the series that pops up is called "The 39 Clues" and there just so happen to be 39 books incorporated into this code!
Hit 'Download Image' for a ludicrously hi-def version of the picture if you're having a hard time making out something in it.
Any questions can go in the comments, and I'll answer them as best I can.

~Tips on solving:
1. Be familiar with the books. People who are will probably figure out parts of this faster than others.
2. Take it one row at a time. You need to solve rows 1 and 3 before getting row 2.
3. It's all about numbers! Numbers and relationships between books. You don't get the letters of the answer until the end.
4. Pay no attention to the half-upside-down cover in the bottom row, that was a mistake. (you'll understand why I say "half" on closer inspection)
5. At some point in the solving process, you will probably have to do some research on the internet, or at home if you happen to own a few things on that bookshelf. It's nothing ridiculous, just a quick googling of the answer to the bottom row. Those unfamiliar with the series that appears most frequently in the picture will also likely have a hard time seeing the pattern in the top row, and may have to do a small bit of research on the series in question to get it right, probably on barnesandnoble.com

If you so desire, you may also use this picture for reference in your quest to find the answer.

Want even more help? Click here.

****And if by some miracle someone DOES solve this, send me a note with the answer! Don't go giving it away in the comments! Please and thank you!****