Thanks for your interest in Alces Flight -
It looks like you're modifying the CloudFormation template to use your own DNS servers, rather than the AWS service configured by Flight Compute as it launches. While that should be possible, you'll need to make sure that the DNS you're using provides all the same functions - e.g. full forward and reverse name resolution for your cluster instances.
Alces often provides consultancy for customers wanting to configure custom solutions, using either existing AWS resources, or on-premise platforms, so it should be possible for you to get your infrastructure to support Flight Compute. Just let us know if you'd like one of our consultants to contact you about setting up a paid engagement to deliver this functionality.
Hope that helps -