Oneye This is my attempt bearing in mind i'm not the greatest ship builder ever
I've armored the reactors so that they don't chain explode and end your ship in one go, I've added a bunch more shields and PD's with alot more crew to back them up, I've also tried to rework the internals to make them slightly more efficient. The head of your ship is now better protected and the tail of your ship is no longer energy starved.
Engine power is the same as before which could be an issue as the ship is heavier now and the FTL is slightly less efficient but that's not as important as survivability and I tried to keep the design as close as possible to the original.
Edit: The reactor near the middle section that's right next to your missile factories is still deadly and a weakspot but it doesn't wipe out the whole ship like before.
Edit2: If you wanted to improve this ship abit more I'd say that the you can replace the electrobolts/lasers/standard cannons with a large cannon or 2, while the intial salvo of the double missile silos is good in the head of the ship it suffers a long term reloading problem because you should have at least 1 factory per silo. I know I removed a missile store there but storage in this game at the moment is not that useful other than to prevent big explosions from happening if you have limited space (unless its missile/ammo storage, that likes to go boom too)