using CloudFormation with an existing S3 bucket

I believe you are mistaken in using CloudFormation to modify your AWS infrastructure. CloudFormation's goal is to create AWS infrastructure in a templated fashion. It has been extended to allow for some management of the resources it creates, but managing existing infrastructure is not it's goal. From the welcome page:

AWS CloudFormation enables you to create and provision AWS infrastructure deployments predictably and repeatedly.

I believe the closest you will be able to get is to set a bucket policy on an existing bucket using AWS::S3::BucketPolicy. Beyond that you can use the AWS CLI S3 API to modify your bucket:

  • put-bucket-acl
  • put-bucket-versioning
  • put-bucket-website