I don't understand why would you choose the default port to be value below 1024 which means you cannot run this on unix system without super user privileges.
Even when I change the port in the config file, it still tries to bind to 999 so the server crashes.
You probably changed the api port.
API runs over 999 TCP per default, unless you change in your config file, nodes exchange data ( transactions, messages ) over 999 udp.
Thats why it tries to bind to 999.
Yes, and that is a design issue, which indicates very poor software engineering skills and lack of experience. Who are these people? Ah yes, they will challenge Intel with their revolutionary microprocessor and create an IoT software ... they just haven't reached the level of a junior programmer ... but they will get there.