I don't want to 'squash' this idea but all the lines that are placed on the Nav/Attack Map when using the Map Tools are code rendered. You can be assured of this as they are unaffected by Zoom levels and are effectively rendered 'above' the game screens. Also, further proof is the fact that there are huge FPS drops when many & long plot lines are placed on the Nav Map, proving they are hardware rendered.
That means that there are no TGA's or Menu1024_768.ini entries that will govern their colour or presence.
Perhaps your last avenue of investigation would be to look at the 'hidden' code. Although there are only a few people in the community that know how.
Edit - There is one last tool to try. DXRipper -
http://www.deep-shadows.com/hax/3DRipperDX.htm, with it you can 'Screen Capture' and export all items that are displayed when using any DirectX application. I propose you try it with the menu bar hidden, a single line plotted, zoomed in and in the middle of nowhere (i.e the least on screen as possible).
Honestly though, unless you can access the Dev code, I really do not think that you will be able to remove the plot lines.
