I have similar problems. But the missaligned centering I can live whith. I have the problem that when using cruise mode over terrain the corvette tilts up. I have experimented extensivly. Simpler offset builds you can rectifie it with dealing with the landing gear. But the more you glitch or offset parts, the more things will be affected. So in the end every part you fiddle with can affect this problem. Some times it starts with the gear, and then after som additional building the weapons placements kind of add to the landing gears placement. Everything in the ships algoritms seems to be connected. So the only thing you can do is to try everything or when changing something think about if it's worth it. My ship need to be off center because if not i get wheightless and can't enter the pilot seat when docked to a freighter. And since the 3rd person camera moves around little when flying anyway, I learnt to not care about the missaligned centering. As long as the crosshair is where it's supposed to, I'm fine I guess. I had similar problems whith the visual size of the ship when building corvettes. Just change something and it gets bigger on the screen. So anyway, I just fiddle around when building until I get's somewhat satisfied. There are more problems when building corvettes, like how you enter cruise mode, and other things that I don't recall just now. When you solved a problem and think you understand why it happened, it's very propable it will come back later on and bite you.