you had to fly it at some point, even if its just to test if the guns work without completely draining your power or if it doesnt fly like a brick. i mean, i get it that when the build is finished, the core is in the tower or a bit to high so it is in a vonurable ( no idea how to write that word, since im not english)/weak spot, but come on.....
figuring that out that the ship is build backwards after 3 weeks of building it, sounds pretty dumb too me to be completely honest.
the best way to fix this is to spawn in this ship in multiplayer, and then ask people to help you build it the right way. although that is gonna cost some time.