Is there any way to Send out email alerts as per rules certain number of days before, if there are delays in closing stories and/or tasks within a ticket
You can use a filter subscription (see https://confluence.atlassian.com/display/JIRA062/Receiving+Search+Results+via+Email)
Your rule will look something like this (e.g. duedate in 3 days - could also be a datetime field )
... and duedate > endofday(2d) and duedate <= startOfDay(3d)
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