Upgrade all the sites so they are all using the same version of WordPress. Be sure to log in to the admin for each so the database tables are updated correctly.
Ensure all the sites share the same database. If they don't, then one way to do this is to dump the db tables to a text file and do a find/replace for the prefix. The important thing is that all the tables for each site has a unique prefix. Then import the tables into the shared database.
Create your hive folder with a fresh install of WordPress, and add in all the plugins and themes that are used in all the sites. If any themes are edited, then I recommend you put them in separate folders. You might want to edit the style.css file to change the name so it can be distinguished for the appropriate site. Edit wp-config.php to add the database info, etc.
Point your domains to the folder. From this point, you should be able to install WP-Hive according to the directions.
You will probably want to edit the wphive_hosts table after the hive is initially set up. Add the unique table prefix set in the 2nd step above along with the corresponding hostname. This prevents wp-hive from trying to auto-create the prefix (and probably getting it wrong).
I think this should do it. Let me know what the result is. Good Luck!!