...Iím already pushing the boundaries of simplicity I originally sought to maintain.
I think this is the biggest problem. You've obviously invested tremendous amounts of thought and creativity into what you've come up with thus far. I think you've tackled some of the problems that at first seemed unsolvable -- i.e. making the ship seem retrofitted from an explorer into a warship -- admirably. And that comes from the person whose design was being covered with each addition -- I think some of the reshaping has been for the better. However, I think it is on the verge -- or maybe has already crossed into -- being overcomplicated. The shell is great, and the articulation is interesting, though it does make me wonder whether it will make the ship appear to be a much smaller craft. Going with a vertical instead of a horizontal orientation is fine because it's different and after all there is no up or down in space. The side "conning tower" is good -- it is an improvement over the observation bubble I had in that spot. The aft thrusters/weapons are great, but here is where we get into the realm of maybe having to make choices. Does it make sense to have all that propulsive-looking detail -- a ring AND a sail AND thrusters tucked in the sail AND the big rocket/guns AND the domes on the bow and stern. If you go with the sail, and you put thrusters in there, maybe you don't need the big, bulging thruster/guns at the aft. OR, maybe you can simplify the sail to be clearly a heat dissipator or radiator alone, and keep the thruster/ guns. If you keep the bulge in the middle then get rid of the ring, or vice versa. In short, "unclutter" the design. It does need to appear a bit "gobbed" up to fit with the backstory, but I think not so much that it actually begins to appear "laden".
I love your renderings and think your mechanical sense is great, but you also have a knack for clean, uncluttered design that I think you need to tap again.