I've always been a fan of Vuescan. Not free, but not horribly expensive either.

Best of luck to you. It's a good thing it scans that fast, otherwise this would be quite a chore. Are any/many of the pages double-sided? My old office had a Scansnap that would scan both sides of every sheet that went through, then at the end it would just delete all the blank sides. Very nifty machine (I might have to think about picking one up).