Thank you for the post.
The following knowledge base article, KB6427, covers the full list of ports used by FileMaker Server 12 Advanced:
Apache/IIS Web Server Default HTTP port 80 is used for access to Instant and Custom Web Publishing. This can be changed by the user configuring their web server and will not affect functionality of FileMaker Server/Advanced other than the port that is needed to access web publishing.
Page 43 of the FileMaker Server 12 Getting Started Guide, talks about deployment troubleshooting when the web server test fails:
"If unsuccessful, the Deployment assistant could not communicate with the web server. This test can fail if your web server requires HTTPS or uses a port other than 80. You can re-enter this information and try to communicate with the web server again."
Is Apache or IIS the web server being used? The instructions to change the port depend on the web server.