Automatic replication on slave node after service restart
Move server-id=3 from under [mysqld_safe] and put under [mysqld]

[mysqld]
datadir=/data/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
symbolic-links=0
server-id=3
[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid
#max_connections
max_connections=400
symbolic-links=0
#skip-slave-start
log-bin=/data/mysql/mysql-bin
#binlog_format=ROW
max_user_connections = 400
key_buffer = 64M
max_allowed_packet = 32M
sort_buffer_size = 64M
net_buffer_length = 64K
read_buffer_size = 16M
read_rnd_buffer_size = 16M
thread_stack = 192K
thread_cache_size = 8
query_cache_limit = 10M
query_cache_size = 64M
innodb_buffer_pool_size = 1000M
innodb_additional_mem_pool_size = 100M
innodb_log_file_size = 10M
innodb_log_buffer_size = 32M
innodb_flush_log_at_trx_commit = 2
innodb_lock_wait_timeout = 50
innodb_thread_concurrency = 16


Then restart mysql

Perhaps [mysqld_safe] does not understand server-id. Normally, options not understood by [mysqld_safe] are supposed to passed to [mysqld]. That's probably broken in MySQL 5.1.