Migrating sites between multisite networks

I have a multisite network that was started pre 3.5 (blogs.dir) on apache. I have a new multisite network set up in 4.0 on nginx running at incredibly fast speeds (I got a 97 on google's site speed). I want to move my sites from the old install to the new install. I used to use Backupbuddy to export / import sites, but it isn't working right now for some reason. Are there other options to handle this? Can cloner move sites to a new network? Anything else?