Running some numbers my suggestion would be:
Forward section: 3 decks x 7.5m wide x 27.5m long = 137tons + 8tons for turrets
Bridge (20tons), Comp (5tons), Staterooms (100tons), 12tons Stores, + Turrets (8tons) = 145tons
Middle section: As per the description leave this an open framework, permitting mounting of and filling in with what the user desires. Cargo modules, fuel modules, small craft, vehicle hangers, etc.
Up to 260tons of gear within 30.0m length
Rear section: 4 decks x 13.5m wide x 33.0m long = 395tons
Jump Drive (65tons), Maneuver Thrusters (23tons), Powerplant (37tons), Fuel 270tons = 395tons
This is just a suggestion to get about the right tonnage allocated in the spirit of the original shape and description. With those as rough guides one should be able to fit deckplans in at the proper allocation without too much work.
For visual interest options:
Forward section: Pop the bridge out a bit (up or down, and to the sides and front) for "better visibility", suck the hull in a bit in some other areas to make up for it, maybe in the commons area at the rear of the forward section.
Middle section: Harder, some kind of truss arrangement of course, maybe just in the center deck, or with a mid line truss span as well. Filling it in is where you can get more creative with different modules and craft.
Rear section: I'm thinking the drives would be on the center deck (for the most part) with the rest being fuel tankage around it, allowing some breakup of the lines similar to the original with the half-split
That's about it...
...I just have to get off my chest how ugly and out of place that dish looks on the front end

(but you know, whatever

)