How to send different logs files to different logstash ports

You can apply tags to the events or use the source field to identify which logs came from which files.

Example using tags:

filebeat.prospectors:
- paths:
  - /path/to/log/type/A/*.log
  tags: ["log_type_a"]
- paths:
  - /path/to/log/type/B/*.json
  tags: ["log_type_b", json]

Then over in your Logstash config you can use a condition to apply whatever processing you would like.

filters {
  if "log_type_b" in [tags] {
     // do something fun like grok
  } // else if ...
}