I think thats the main issues,....but it all stems from your last point,...its all messed up because they got the height wrong,....the moved & manipulated all key areas around the ship to try & fit everything in,...there's also the jaw boxes which are too wide & thick, & the cockpit walkway angle is wrong, the radar dish is too small (I got a new larger one crafted by Scratchy.....way before 3d printing ones became available)
J