Optimize database tables in one site of wordpress multisite

Hello. I currently have a wordpress mulltisite with about 100 sites BUT later tonight I will be deleting and re-cloning all the sites. I want to have the master copy site completely optimized so that the cloned copied will be as lightweight as possible. I would also like all the sites to use the same media files from the master site so those wont be cloned in every instance. We are expecting THOUSANDS of sites so this must be optimized to the best possible. Freelancer MUST know what they are doing and not cause anything to break.