I’m not aware of any limitation with length of secrets, though there likely is a limit.
I’ve stored some SSL certificates that are base64 encoded into secrets with no problems.
Have you narrowed down when the crash occurs? Does it occur when the VM is being provisioned? Or does it happen after your code has started executing?
You can get a real time view of whats going on by running fly logs in one terminal then running fly deploy in another terminal.