I'll start with the easiest stuff.
The rotating "sensor" thing is just actuated blocks hooked up to a one second timer. As one side actuates, the other activates, so it gives the illusion that it's moving.
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The ship's guns are just a few portal stations hooked up to a one second timer. The timer feeds into a logic gate that has four inactive, one active, and a faulty logic lamp. That way, the gun won't fire every second, but it will fire fairly frequently, somewhat at random.
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The sliding doors are fairly simple. The blocks that act as the door are hooked up to actuators. Each block has a different wire color. You connect each of those wire colors to a separate teal pressure plate surrounded on either side by dart traps, evenly spaced. Between the dart traps and the first pressure plates is an actuated block, and an active block. When you press the input, both dart traps shoot. Since one side is blocked with an actively solid tile, only one dart can reach the pressure plates. As the dart travels from left to right (or right to left) it actuates/activates the sliding door's blocks in order, giving it a moving appearance. It also swaps which block is active in front of the dart traps, so that the next time you send an input signal, the pressure plates are triggered in the opposite direction. It might sound complicated, but it really isn't. Here's a screenshot that shows what the door's "engine" looks like, and directly below it is how the door would be wired up.
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The reactor is going to look complicated, just based on the screenshots, but I assure you it's mostly just clutter. The concept is very simple. Here is what the wiring at the reactor itself looks like.
Basically, the reactor is made up of a bunch of inactive gemspark blocks. As wires activate them, they "separate" from the inactive blocks, and light up. The wires are arranged in a specific color pattern. Starting from one side, using one color, draw the shape that you want the moving light to be. In this example, I used a 2x2 square.
Here's another example of a reactor that I'm using with a different light shape (diagonal).
After you've drawn your pattern against the gemspark with one wire, move one tile to the side, then draw the exact same pattern with a different color wire. Repeat this process until all of the gemspark blocks are covered in your wire pattern, and make sure to always use the wires in the same order to make it easier to remember. For example, my reactor from left to right uses blue > red > yellow > green.
Next, you run all of this massive amount of wires (there are a TON of wires, so be extra careful not to cross any of them) to the following "engine." This is just a small segment of the engine (it's quite a bit longer, but it's all more of the same thing, so no need to show it all).
On the left side of the screenshot shows you what it looks like without wires, and the right shows you with wires. Basically, it's a simple pattern. A spear trap is activated by your initial input (in my case it's triggered by player sensor when they first arrive on the ship). That spear trap shoots a teal pressure plate which deactives the logic lamp behind it, activates the logic lamp in front of it, and activates the spear trap in front of it. This allows the signal to be passed in one direction.
When the logic lamp in front is activated, the AND gate it is connected to is turned ON, which activates the gemspark blocks. When the logic lamp behind the pressure plate is deactivated, the AND gate it is connected to turns OFF, deactivating those gemspark blocks. That means only four gemspark blocks (in this 2x2 pattern example) will be active at a time. As the signal travels up the line, the block of light travels down the reactor.
When you are connecting your wires to this engine, you can choose which direction your reactor lights move. In my example, you can see that my wires are connected from bottom to top in the same order that I used on the gemspark blocks (blue, red, yellow, green). Because you don't want to cross any wire colors, you will have to change what colored wires you use for your input lines (connected to every teal pressure plate) every time you change your output lines (connected to the AND gates).
If you want one side of lights to move in the opposite direction, like mine do in this example, you will have to make sure that the bottom half of the reactor's wires are connected to AND gates in the opposite order of the top half.