Ok. So here are today's changes.
I've made the changes to the pylons as Adonis suggested wich, as I mentioned earlier, messed up the lower part of of my secondary hull. So I have redone that too.
Now I've removed the smoothing groups from the body of the ship for now, except for the redone secondary hull. Cut the ship in half, copyed the remaining half and mirrored it, attatched it so I have two perfectly mirrored halfs (yes... I remembered to collapse the duplicate vert's into each other
).
Total Polycount is now: 1898
(EDIT: This did'n seem to work. So i fixed it)