How do I properly configure my cloudwatch.config file after upgrading from Amazon Linux 2 v4.5.3 to Amazon Linux 2023 v5.1.8?

Hello.

Can you confirm that the CloudWatch Agent is running on your EC2 instance?
Also, check the CloudWatch Agent logs to see if any errors are output.
https://docs.aws.amazon.com/AmazonCloudWatch/latest/monitoring/troubleshooting-CloudWatch-Agent.html#CloudWatch-Agent-files-and-locations

/opt/aws/amazon-cloudwatch-agent/logs/amazon-cloudwatch-agent.log or /var/log/amazon/amazon-cloudwatch-agent/amazon-cloudwatch-agent.log

files:
  # ####################################################################################################################
  # First we create a custom config file that lists additional files that should be included when we request
  # "Last 100 lines" of the logs (not just when we select "Full").
  # Note: Several other files are included by default.
  # This ".conf" file is picked up automatically since it is added to the taillogs.d folder.
  # See: https://docs.aws.amazon.com/elasticbeanstalk/latest/dg/using-features.logging.html
  # ####################################################################################################################
  "/opt/elasticbeanstalk/tasks/taillogs.d/my-company-tail-log.conf" :
    mode: "000755"
    owner: root
    group: root
    content: |
      /var/log/cfn-init-cmd.log

  # ####################################################################################################################
  # We also create a custom config file to specify that the application.log file should be streamed to Cloudwatch,
  # (in addition to other files that are streamed to Cloudwatch by default, like eb-engine.log, eb-hooks.log etc)
  # This ".json" file is not picked up automatically, but we point to it in the container_commands below.
  # ####################################################################################################################
  "/opt/aws/amazon-cloudwatch-agent/etc/my-company-amazon-cloudwatch-agent.json":
    mode: "000600"
    owner: root
    group: root
    content: |
      {
        "logs": {
          "logs_collected": {
            "files": {
              "collect_list": [
                {
                  "file_path": "/var/log/tomcat9/application.log",
                  "log_group_name": "`{"Fn::Join":["/", ["/aws/elasticbeanstalk", { "Ref":"AWSEBEnvironmentName" }, "var/log/tomcat9/application.log"]]}`",
                  "log_stream_name": "{instance_id}",
                  "timestamp_format": "%Y-%m-%d %H:%M:%S.%f"
                }
              ]
            }
          }
        }
      }

# ####################################################################################################################
# Note: The execution of the commands below is logged in file cfn-init-cmd.log
# ####################################################################################################################
container_commands:
  "01":
    command: |
      sudo /opt/aws/amazon-cloudwatch-agent/bin/amazon-cloudwatch-agent-ctl -a fetch-config -m ec2 -s -c file:/opt/aws/amazon-cloudwatch-agent/etc/my-company-amazon-cloudwatch-agent.json

This is what my coworker ended up using which worked for populating the cloudwatch logs. There are some comments that explain what's going on in this config file, but I don't understand it enough to explain it, so I will leave this question unanswered. If anyone can explain why this is working in a comment I will accept this answer.