1. ERROR 2049 (HY000): Connection using old (pre-4.1.1) authentication protocol refused
Reason:
This is not a bug if you have user accounts with passwords that used the ancient old hashing algorithm. If you read the bug report mentioned in the link you posted:
http://bugs.mysql.com/bug.php?id=69027
Resolve Method:
Modify the my.ini
[client]
secure-auth=off