You can manually create connections between ports via REST, and if you'd like and then lock the connections in place I think you can use the attribute LockConnection (0x129f1) if you are sure that they are correctly configured.
For a correctly configured connection between two ports (Port1 from Device1 and Port2 from Device2) you have to create the following associations:
Port1->Port2 (Links_with 0x00010023)
Port1->Device2 (Connects_to 0x00010005)
Port2->Port1 (Links_with 0x00010023)
Port2->Device1 (Connects_to 0x00010005)
You can then automatically identify connected ports by the attribute NetworkLinkType (0x12a79). You can use this to be search criteria for a GC and activate a monitoring via Policy.
That is, if I understood correctly what you need.
I did a similar system that connects ports based on their Internal_If_Alias and assures automatic active/passive monitoring for all connected ports.