Update: I finished building the box in the meanwhile leaving out the audioin-jack just to check if I did right. What I mentioned in my first post seems to be still an actual problem. The connector-cable attaches to the mainboard only very loosely. When I boot the Zynthian (whether the cable is attached to the mainboard or not) the 4 controller knobs don’t work, though everything else does (audio/midi).
I think I might have done the same thing wrong as this guy Module PCB: solder side problem? 
Does the side of where the longer pins stick out really matter that much? Wasn’ t clear to me what the upper or lower side of that part was.
The controller knobs look like they’re all soldered right as in the pictures, so I think the problem isn’t there.