Hi Nathan,
I had a similar problem but with far less pages than you're talking about. I think notifying Google Webmaster Tools is always a good idea and that's what we have done here but it took a few weeks in our case to see any results but I'd like to think that the few weeks were better than without taking any action.
We also used 301 to redirect because that was highly recommended by everyone in our team.
All the best!
Alex