@big fish I added two manipulator beams between the hyper drives in the back. I find them quite useful. I also added mining lasers to the front middle instead of extra storage, but someone pointed out about turning some of the factories so I might add some storage back.

The manipulator beams could also enable ressuplying in battle without having to use crew to carry the ammo/missiles

You could also make a battle configuration, where you could remove some of the factories, you might not really need in battle (like the second diamond maker thingy) and instead exchange them for more storage or crew. And also add manipulator beams to the ship design, its quite a pain to do it yourself on a complex design made by another person.

Can I use your ships in some faction mods I'm making?

I will add links to your mods and your name so you get the credit.

Yeah I would like to confirm twisted' statement about the 2 engine rooms connected to 1 huge thruster. The bonus stays 50% if you have 1 or 2 engine rooms connected to it. So basicly its a waste of resources. Also you don't need to have doors on your thrusters if you have engine room, the engine room does all the powering so you don't have to place doors.

Also the factories are placed to far appart for my taste. I like them all in one block, since every adjacent factory gives bonus to certain factories. For example I have the steel, tri steel, coil, hypercoil, uranium enrichment, processor and diamond in one block, the ammo and missiles in another. If you place them just right you can get 100% bonus in steel and tri steel factories.

Like this: (from left to right, top row) uranium, tri steel, processor
(bottom row) hypercoil, steel, coil.
diamond on the side between coil and processor. and you got 100% in steel and tri steel factories

It looks good though there are some things I would like to suggest. You could place either a capacitor or reactor midway where there are two hyperdrives. Since it requires energy in order to do a hyperspace jump and currently its quite far away from closes energy source. Another thing is that you have two engine rooms on each side in the back. I dont know if two engine rooms on one thruster gives 100% increased but if not it probably would be better to move one engine room to cover the small and the big thruster. Also the 3x4 factories could be turned sideways as its still only possible to access them from one corridor. The "leftover" space around 3x3 factories can be used for airlocks and fire extinguishers midship as its quite far to the closest one.