I am not sure how to fix this:
dyn-72-33-214-45:python mona$ sudo /usr/local/mysql/bin/mysqld stop
2014-09-06 09:49:04 0 [Warning] TIMESTAMP with implicit DE
The MySQL daemon should not be executed as the system user root which (normally) do not has any restrictions.
According to your cli, I suppose you wanted to execute the initscript instead:
sudo /etc/init.d/mysql stop
Another way would be to use the mysqladmin tool (note, root is the MySQL root user here, not the system root user):
/usr/local/mysql/bin/mysqladmin --port=8889 -u root shutdown