How to Parse my JSON stack trace in logstash?

Assuming UTF-8 encoding, your original payload is 5,490 bytes, and the output your are seeing in Loggly is truncated at exactly 1,024 bytes. It looks like something is truncating your message at 1KB.

Which version of Logstash are you using?

Meanwhile, try changing your configuration in this way, and see if it changes something:

input {
  file {
    path => "FILENAME"
    start_position => beginning
    codec => "json"
  }
}

output {
  loggly {
    key => "loggly_token"
    tag => "logstash"
  }
}

Using the json filter is not necessary, if you provide a codec to the file input. This will leave your payload in the message field, and it will be shipped to Loggly in this way.