I tried to use WebSphere Configuration Migration tool which instructed to issue an wsadim command to capture configuration in property file which when imported into the tool gave server.xml file with only jsp-2.1 feature. How do we shift all the resource configurations? I was not able to see any DB, LDAP and JMS configurations that got migrated.

WCMT does migrate resource config for DB, LDAP and JMS.  It would help if we could view the content of the properties file to give us a better understanding of the issue.