Your question about the port might depend on how you plan on using the S-Parameters. If you define signal and ground pins with the ports, then your S-Parameters will be specific to that connector configuration. If your client only cares about that one specific configuration of the connector then that is the easiest option. If you are truly trying to characterize the connector for any configuration, then you would need to have a different port for each pin, that includes the pin and some common reference point (Chassis or something similar). The second setup would produce 24x24 different S-Parameters, that fully characterize the relationship between each pin (24 for each end of the 12 pins). That setup would be a lot harder to get working, but is more complete. You will have to determine what is sufficient for your client.