<?php

$str = 'SET VERSION=3
SET BACKUP_DRIVE=D:\
SET BACKUP_DIRECTORY=BACKUP\
SET HOURLY_DIRECTORY=HOURLY\
SET INPUT_DIRECTORY=C:\MySQL\Data\CDR\
SET username=username
SET password=password';

preg_match_all('~^SET\s+([^=]+)=(.*)$~m', $str, $matches);

$params = array_combine($matches[1], $matches[2]);

var_dump($params['username'], $params['password']);