Starting Over

I am currently hosting a Network install (with Buddypress) that I originally created with version wpmu 2.7. In comparison with my newer 3.1 Network install — where things run a lot smoother — I feel like somewhere along the upgrade process things have gone astray. Example: In the 2.7-3.05 version, as the network admin, I need to log into every subdomain blog I want to visit, and yet on the 3.1 install, logging into the main domain, gives me logged in access to all of the subdomains. Pair that with the deprecated notices of a site that has code from before the 3.0 merge, and I’m wondering what it would take to start fresh.

If I took a fresh install, and pointed the wp-config.php to my existing database (750 users, 500+ sites)

Pulled in my wp-content themes and plugins, my mu-plugins folder, and my blogs dir folder, would my network survive? Am I forgetting something huge?

Is there something easier I could do? My wp-config file looks a heck of a lot different than the fresh install, maybe I just need to regenerate that?