Use a CATALINA_PID file and the -force switch... https://confluence.atlassian.com/display/JIRAKB/JIRA+Does+Not+Terminate+after+Shutdown+Script
There doesn't seem to be an actual question here?
The error message you're getting there happens when the Tomcat running Jira is either dead already, not listening (have you changed the config?) or has failed. You need to read the catalina.out to find out what it's doing.
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