Here is the improved ship:

I tried to change the aesthetic as little as possible.
Cost: $1,237,950
Crew: 241
Weight: 1191.9 Tonnes
IMPROVEMENTS:
-Removed Thrusters
-Added Different Thrusters
-Changed Thruster layout
-Removed some Reactors
-Removed all Reactor Storages
-Removed some Crew
-Compartmentalized interior
-Added Fire Extinguisher
-Added Ammo Factories
The completed ship isn't outrageously better than the original, but that's because I didn't touch the weapon layouts and made sure not to change the design of the ship on the outside.
Obviously, if you want to change it more drastically, feel free to (after all, it's still YOUR ship) 🙂
Hope this improved ship benefits you!
xPLAYn