Sometimes I like to just delete everything in MySQL and start over. This is easy in Linux when you have the packaged script "mysql_install_db.pl" but we need to do it in Windows too.
After you delete everything in the \data directory, go to the command prompt, from your MySQL \bin directory:
mysqld --skip-grant-tables
Then open a new command prompt in the \bin directory and connect to your instance:
mysql
>create database mysql;
>use mysql;
>\. ..\share\mysql_system_tables.sql
>\. ..\share\mysql_system_tables_data.sql
>exit
Now, shutdown your server daemon:
mysqladmin shutdown
You should be able to restart the daemon:
mysqld
and login as root to begin configuring your permissions:
mysql -uroot