I wouldnt recommend starting from scratch. You could use FLHook and extend the plugin calls for sending network packets (make sure to commit it to the sdk on the svn) and suppress the calls to HkIServerImpl.

That way, you can implement your own logic while still using the native Freelancer network protocol (which isnt too bad). Replacing the whole network layer as well would be a massive undertaking which you dont just do within a year in your free time. Replacing the actual logic and reversing more network stuff is already a huge task and I also dont think you can do that in a foreseeable timeframe. But that would be the most straight forward approach IMO.