So, let's talk about craft.
This system is not final. If you are have ideas about how to make it better, you are free to express it and let's try to make it better together.
Basic resources
First you need to gather basic resources. Now you can get it from asteroids. In future you will be able to extract it from planets.
There is a full list of resources for now:
Carbon
Aluminium
Silicon
Silver
Titanium
Iron
Cobalt
Nickel
Cuprum
Niobium
Oxygen
Hydrogen
Xenon
Ice
Fullerite
Deuterium
As you can see, we decided to not invent anything and implemented real elements.
Processing
Then you need to build a module to refine these resources.
Any metal ore → Refined metal
Ice → Oxygen and Hydrogen
Hydrogen → Deuterium
Carbon → Fullerite
There will be several resource processors:
electric furnace
water electrolysis module
Each processor unit require power to work.
Power is generated from solar panels and generators. And generator required a fuel.
Parts
Then you need to build modules parts. There is full list:
Metal Plate
Tube
Electric motor
Wires
Battery
Capasitor
Control circuit
Fasteners Kit
Armored Plate
Magnet
Superconductor
It can be builded in production module from refined resources.

And finally, engineering drones can assemble ship's modules from these parts.