Hi VivaciousWalrus99 ,
If you're using Trains Server in it's default setup (i.e. not using a load balancer and subdomains), you can only change the port numbers for the Web interface (8080 by default) and the Fileserver (8081 by default). The API Server's port (8008) should not be changed (we plan to change that in future versions).

By the way, we are planning to address this issue soon...

How can you trick the machine to think it is another port? i.e, put a "port in the middle". That the api server port will think it communicate to 8008 but that it will actually communicate to a middle man, which will port on another port?

The best way to do that is simply use a load balancer with subdomains - it will be much safer and won't require any hacks. Are you running your Trains Server locally, or on the cloud?