Is there anyway that I can manually create a PID for the MySQL instance?
No, you do not want to go there. Why ?

The mysqld_safe script is responsible for creating and destroying the PID file

You can see it when you grep for it

$ MYSQLD_SAFE_SCRIPT=`which mysqld_safe`
$ grep -n pid_file &lt; ${MYSQLD_SAFE_SCRIPT}
26:pid_file=
198:      --pid-file=*) pid_file="$val" ;;
638:if test -z "$pid_file"
640:  pid_file="$DATADIR/`hostname`.pid"
642:  case "$pid_file" in
644:    * )  pid_file="$DATADIR/$pid_file" ;;
647:append_arg_to_args "--pid-file=$pid_file"
720:if test -f "$pid_file"
722:  PID=`cat "$pid_file"`
731:  rm -f "$pid_file"
732:  if test -f "$pid_file"
735:$pid_file
782:  rm -f $safe_mysql_unix_port "$pid_file"   # Some extra safety
796:  if test ! -f "$pid_file"      # This is removed if normal shutdown
834:    numofproces=`ps xaww | grep -v "grep" | grep "$ledir/$MYSQLD\&gt;" | grep -c "pid-file=$pid_file"`
840:      PROC=`ps xaww | grep "$ledir/$MYSQLD\&gt;" | grep -v "grep" | grep "pid-file=$pid_file" | sed -n '$p'`
859:log_notice "mysqld from pid file $pid_file ended"
$


What you should do is

service mysql stop 
... delete the pid file if it is still exists after shutdown
service mysql start


If you have to restore backups from MySQL Enterprise, make sure there is no PID file.

Preferably, you could setup MySQL Replication and do the backups on the Slave. Then, when it is time for backup, run 


STOP SLAVE;
SET GLOBAL innodb_fast_shutdown=0;
service mysql stop (The pid file should get deleted by mysqld_safe)
Make your backup
service mysql start (The pid file should get created by mysqld_safe)


CAVEAT

If you ever have a problem with service mysql stop taking forever and still not shutting down mysqld, this quickly indicates that the socket file is missing. PID file will be out of whack as well.

In that happens, do a TCP/IP shutdown of MySQL

First do this

mysqladmin -uroot -p -h127.0.0.1 --protocol=tcp ping


If this echoes

mysqld is alive


then you can run

mysqladmin -uroot -p -h127.0.0.1 --protocol=tcp shutdown


GIVE IT A TRY !!!