Here is the improved version against your original:

And here is the improved ship:

Cost: $2,864,500
Crew: 326
Weight: 9831.0 Tonnes
IMPROVEMENTS:
-Compartmentalized most of the ship
-Added Point Defense
-Rearranged Shields
-Added more Shields
-Moved the Crew and Reactors to more convenient places
-removed all Reactor Storages
-Added some Super Armor
-Added more Thrusters (for reverse)
-removed some Ion Beams
Overall, this ship is now virtually indestructible towards your previous version. The shields recharge so fast that it can't even break it, and the ion beams never shut off (unless the enemy ship drifts out of range). The inclusion of a Super Armor skin makes it a much better ship, and the reverse thrusters improve maneuverability handsomely.
I hope this helps 🙂
xPLAYn