VDU settings are all in the ship file as well. Check out Killerwave's site for a full tutorial. Basically there are numbers in the ship file that point to a mat file to use as a VDU image, and also to a Target ID string.
As for afterburner flames, you cannot edit their sizes or shapes, since nobody has found out how to... so you can only use stock WCP flame meshes. Take a look at WCP data files, usually any mesh with "aft" in its name is a flame mesh, though there are exceptions that will crash the game if you try to use them. The name of which mesh to use is also something that you put in the ship file.