I have jenkins.war and I started it from command prompt in Windows as:
java -jar jenkins.war
It was started well and easily browsed as
For Fedora, RedHat, CentOS and alike, any customization should be done within /etc/sysconfig/jenkins instead of /etc/init.d/jenkins. The purpose of the first file is exactly the customization of the second file.
So, within /etc/sysconfig/jenkins, there is a the JENKINS_PORT variable that holds the port number on which Jenkins is running.