my.cnf become with default configuration and you need write your config with posted examples. You dont need remove innodb_data_file_path... at first config of innodb remove ib* files from /var/lib/mysql, and when mysql start will recreate then again with your config.
IMPORTANT: Never do it with a production innodb tables in DB, you only can remove innodb files with a clean DB without innodb tables... if you want to change some important config of innodb, you need dump all your data, remove files, change config, restart mysql, and reimport all.
To webservices... a LAMP in linux is the best solution =)
Best regards