The optimization process and recommendations:

1. Avoid Calling Functions With Indexed Columns (query line: 25): When a function is used directly on an indexed column, the database's optimizer won’t be able to use the index. For example, if the column `shift_start` is indexed, the index won’t be used as it’s wrapped with the function `date`. If you can’t find an alternative condition that won’t use a function call, a possible solution is to store the required value in a new indexed column.
2. Avoid Calling Functions With Indexed Columns (query line: 26): When a function is used directly on an indexed column, the database's optimizer won’t be able to use the index. For example, if the column `shift_start` is indexed, the index won’t be used as it’s wrapped with the function `date`. If you can’t find an alternative condition that won’t use a function call, a possible solution is to store the required value in a new indexed column.

The optimized query:

SELECT
        secud_id,
        secud_fname,
        secud_sname,
        users.user_id,
        users.user_owner,
        users.user_level,
        shifts.shift_start,
        GROUP_CONCAT(DISTINCT uq_name SEPARATOR ' ') quals 
    FROM
        user_data 
    INNER JOIN
        users 
            ON user_data.secud_ulink = users.user_id 
    LEFT JOIN
        user_quals 
            ON users.user_id = user_quals.uq_user 
    LEFT JOIN
        shifts 
            ON shifts.shift_user = users.user_id 
    WHERE
        users.user_owner = 2 
        AND users.user_level = 'Personnel' 
        AND (
            date(shifts.shift_start) <> '2016-03-16' 
            OR date(shifts.shift_start) IS NULL
        ) 
        AND users.user_active = 1 
    GROUP BY
        users.user_id 
    ORDER BY
        secud_sname ASC