Add a DelelionPolicy attribute to the S3 bucket resource, with the value Delete forcing the bucket to be removed when the stack is deleted.

Add a custom resource with an AWS Lambda function with the DependsOn attribute specifying the S3 bucket, and an IAM role. Write the Lambda function to delete all objects from the bucket when RequestType is Delete.

Identify the resource that was not deleted. Manually empty the S3 bucket and then delete it.

Replace the EC2 and S3 bucket resources with a single AWS OpsWorks Stacks resource. Define a custom recipe for the stack to create and delete the EC2 instance and the S3 bucket.