Thanks for being nice.

My limited knowledge made me think about something like tftp which uses UDP and is very lightweight. I mainly used it to debrick my router, but I'm a network idiot in general.
But there's a slight misunderstanding: aMule(d) will run as ever. Nothing about two servers, only one server as always.
But: You can
copy the files from/to aMule Incoming folder via EC (ec is intended to be the control protocol, and something like tftp for the data flow -> network idiot, see above).
Example: I want to publish my Nexenta aMule deb package and have a Linux amuled server running.
First thing is downloading the aMule source code via ed2k. Now I have the source code on my Linux server, but I have to copy it on my machine. Either I open another program to copy the source or I would simply use the remote GUI to save the file on my machine.
After building the package, I want to publish it. Now again, I have the package on my machine, but I want it on the server. Either I use ftp/... to copy the file or I publish it using the GUI, without involving any other application.
Whoever runs an dedicated amuled-server doesn't use the files on said server
Explanation: You wouldn't listen to music or watch a movie on a server without X, will you? You'll rather use your desktop PC or notebook, maybe even running windows.