Vecktor, this is a magnificent job. I love the way the added details are providing scale and character to the original design. One idea that occurred to me is this... Since the ship has be hastily modified for combat duties, should the modifications have a more bolted on, patchwork, bare metal appearance to indicate aesthetics and matching the original paint scheme were not a priority during the refit?
As for the warning markings, go for it. Some red outlining like you have around the lander wouldn't hurt. As far as I'm concerned only in PC Star Trek do combatants have the luxury of targeting specific systems like engines or weapons. In real combat you are just aiming for center-mass end of story. If an enemy can read the markings you have added so far, they are too close already.
Those are my two credits worth.