I am really digging the detailing around the FTL drive "bubbles". With the flaps open, the structure reminds me of a Serenity but with a clean 1960's scifi spin to it. Awesome work.
But on the other hand... and I hate to say this... I don't like the new fins. To me they disrupt the natural "flow" of the engine cowling and make the sides of the craft to visually "busy". I also think the sharp angles don't fit well with the curves featured everywhere else. But if you are intent on keeping the fins maybe you could move the angle from 45 to 90 degrees so the two fins are parallel with each other. I would also suggest shortening them a bit. That may give you the look you are after while keeping things more uniform.