Would it be possible to generate a random map until you get the general shape you want, place systems, fleets in good locations, and then save it that way? If systems are what you can't change, can you change the terrain? If so, I would really think thist would be the way to go.
I don't think people will get too mad if you can't have the exact set up you want, just a map with the relative postitions to be accurate. It will still be loads of fun to play even if all the systems aren't excatly where they should be.