Run multiple MySQL instances in Windows
Easy, with MariaDB.

mysql_install_db.exe --service=service_name --datadir=datadir --port=port

Run this multiple times with  different parameters (service_name, datadir, port should b different for different instances). Start services with "net start " . 
This is supported official tool. Documentation is here https://mariadb.com/kb/en/mariadb/mysql_install_dbexe/ . You do not need any mysql_multi, really :)