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If you look at the running EC2 instances you will see a bunch of running EC2 instances in the elastic-beanstalk security group without names. To find the name, go to the running Beanstalk environment and and click on logs -> snapshot logs to get the console to tell you the name of the underlying instance name: 
From this point, you can then go to the list of running EC2 instances and find your particular instance using the browser's find function. Note that you can rename the instances to match the beanstalk environment name, but that beanstalk recycles instances and will eventually replace your named instanced with a new one.
Where is the WAR file?
The servlet WAR is expanded under:
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For links to more documentation and info about the ssl cert see PLFM-142 142
Gotchas Getting Started with Beanstalk
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