When you reinstalled JSD, what version is installed? What version was previous installed for Jira and JSD before this?
If you're not seeing the Cog Icon -> Applications -> JIRA SERVICE DESK: Configuration, then I think either the JSD plugin is not licensed and in turn is not starting up, or the plugin itself did not startup when Jira started up. But if that happens, the $JIRAHOME/log/atlassian-jira.log should tell us more information about whether or not JSD has started up correctly or not.
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