No WPMU plugins working after 3.0.1 upgrade

Well after a misfire on getting my WPMu site going, WP 3 came out. So I hit the upgrade button and now think I have stopped all the plugins working. I get the following error message:

Sorry, we can't find the content you're looking for at this URL. Please try selecting a menu item from above or to the side of this message to get where you'd like to go.

Now would it be easier to just wipe the install completely and start from scratch?

I have looked everywhere (obviously missing the right FAQ, tutorial) to see how I should have done this.

Thanks in advance!