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You're question is a little vague. You could do this all on 1 EC2 instance, depending on the load. You can install Java, and MySQL on a single linux instance. Weather this will work for you or not, depends on the app. load, the size of ec2 instance you use. Many things.
As for creating your own linux image, yes you can do this, there are many articles on the web detailing this, a quick google search turned up this one http://computeretal.blogspot.com/2010/05/create-amazon-machine-image-from.html
Good luck!