Aye, reduce the height down a layer of bricks (maybe cut the bricks to be smaller too, but that's just my opinion). Some balsa supports could break up the brickwork a bit, along with random rubble/ loose bricks (for cover), moss, damp, random ground scatter / furniture, torches, paintings, rugs, etc.
6'' by 6'' suits for typical skirmish game movement, and saves on pieces. I went for 4'' by 4'' myself, but that's because I wanted mine to be more modular. In my own setup I've found T sections, followed by Ls are the most common parts. Straights and dead ends are rarely used because all of the Ts.
96 pieces sounds like a lot. If you're doing that many you'd either want to mass produce loads of small sections (then do a second pass adding random details), or create some larger rooms (with more time spent on the contents, like barracks, temples, cells, etc).