Starsuperion ... beautiful work again!
I hope you forgive me for doodling over your graphics, but it's easier to discuss things if I point out the sections I'm talking about.
I almost get the sense that the sections highlighted in gold below are intended to move:
As modules in the central core are added and jettisoned, do the upper and lower sections move up and down while the shield generators move in and out?
I think this design is starting to inspire a sense of grace and beauty again. My only complaint is that the areas highlighted below in green seem to be too straight along the edges:
I've added a simple circle around the structure to indicate a possible field of force around the ship. The actual shape of this field can be anything and is probably more complicated as you've indicated in other illustrations. But I'm using a simple circle for discussing a design suggestion only. What if the edges of the upper and lower sections curved to follow the proposed field of force rather than sloped directly between a larger and smaller diameter structure? I'm a big proponent of form following function, and the lines of force of a magnetic field (for example) are beautiful curves. Any structure that followed such lines of force (presumably for some super-science purposes) would also reflect that beauty and bring to mind a technology melded with nature.
Finally, I have one final image to throw out at you:
That cityscape is somewhat iconic. And I'm fascinated with the sphere surrounding the city. I wonder if the original intent was to make it reminiscent of a snow globe or Christmas ornament. It's just a wild idea intended as nothing more than brainstorming, and I'm in no way trying to tell you how to build your fleet, but what if TARDISes looked, in five dimensional space, like glittering Christmas ornaments with golden arches and crystalline spires?