Calibre. Without question, calibre. You'll need it just to organize, categorize, and make sense of that many books, and sort out which ones you want to put on your reader, which are duplicates, which are the same book in different formats, and so on. Trust me, it will save your sanity.
If the books on the DVD are legit, I might be interested in that myself. Six bucks seems like a very small price to pay to avoid hours of time locating and downloading ebooks.