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MySQL 4.0.x is not currently required, but is highly recommended. On a larger site, 3.x's inability to do descending sorts on indexes will hurt performance in a number of places. The introduction of the inverse timestamp field to the cur table and old table was a partial workaround for this. It may at some point be removed, in which case performance would really suck on 3.x for things like history lists and contribs in particular.

The fulltext search can also use the boolean search mode in MySQL 4.0. Set $wgDBmysql4 = true in LocalSettings.php to activate this mode, which should be faster and more flexible than the manually created parser.

Note that you should avoid versions of MySQL 4 prior to 4.0.13 due to various bugs.

You may wish to adjust the settings on the fulltext search for the stopword list and the smallest indexed word. Check mysql docs for that.

"Q: Must/Should this be done as the OS root user?"

1. initialize the database

mysql_install_db 

2. start sql server by

safe_mysqld

or

mysqld_safe

3. test it by

mysqlshow

4. set up user password

mysql -u root

The prompt 'mysql>' should appear now Choose the right database with user account table

use mysql;
update user set Password=PASSWORD('mypassord_here');
flush privileges;

Note: be aware the ; after the last command, it is required for standard SQL statement This will set all user's passwords to the same one. It is a quick but dirty solution. For more advanced solution, refer to http://www.doctaur.com/dtdocs/databases/mysql-manual/securing-the-initial-mysql-accounts.html

5. shut down the server

mysqladmin shutdown -u root -p

Input the password to shutdown

6. connect the sql server in console and enable SQL query mode

mysqld_safe -u root -p

Input the password to proceed

See also ugly MySQL hacks, old Upgrade to MySQL 4.0 page.

References

mysql post installation tasks/configurations http://www.doctaur.com/dtdocs/databases/mysql-manual/unix-post-installation-procedures.html