When you are in the upper deck (lvl47)
coming by the teleport, go to the south, there is a door called "engineering"
you will need a control cube to open it
then use the gear key to open the next door in the south (called shuttle bay)
you will find another key to open the "command central" door
by the way, the control cube is located in this level, south west, "fuel tank 1"
finally you will get a key, a control key, to open the control area in the factory (lvl20), after cleaning the spaceship you need to return back to the factory.
then you will need another control key, the second one is located in the level 23, in the experimental lab. I Don't know if you have already found it. But you must pass the fusion reactor and the shooting range test. These areas can be accessed by going trough the experimental forge sector, west of the factory, lvl 20.
I know, this is huge
, when i stuck again i´ll return here. 