This isn't an answer for how to get your files back. This answer is how to make this be no big deal the next time it inevitably happens.
You should treat EC2 instances as being disposable. That means that you fully expect an EC2 instance to go down, so you design your application and deployment strategy around that fundamental concept.
Your deployments should be from the latest copy of your source code form source control (e.g., Git, SVN), and should be 100% automated other than kicking off the process.
Next, don't store important data on the instance (unless you keep it on a persistent EBS volume). Keep the data either in S3, on an EBS volume. Enable versioning in S3, take regular snapshots of your EBS volumes.
Since there is a 100% chance of something bad happening to an instance in the future, plan ahead, and make sure you're treating your instances as disposable compute units.