How to fix Buddypress lag and database repair when coming back from multiblog?

When I started my multisite I wanted to have the same userbase and groups in buddypress for all sites on the installation so I set multiblog to true in the settings file. After a year of use and around 1,200 members, I needed to turn the buddypress installations back to singular and set multiblog to false. The two secondary sites function fine and have a good speed but the main site is slower and things like the "load more" button and buddypress specific functions are extremely slow. How can I rebuild to get my speed back?

Multisite installation
Dedicated rackspace cloud server for the files and a separate rackspace cloud server just for the database.