JD,
As one who works for the major DB company, I'd be happy to do whatever it takes to get you to use a real database, as opposed to flat files. True, there is an extra effort associated with the setup, but the improvement in flexibility you'll obtain is huge. And judging by the amount of design help you're getting from this board, you will undoubtedly be changing and adding to the system over time.
I'd be happy to help with the database side of this project...
Jim