I checked, the brown wire was indeed shorted to ground. I pulled it out of the connector and the few minutes I let the bike running it seemed to run just fine. Before though, after changing the cdi box and stator, it seemed to run fine for about a day until it wonked out, so I am excited but a bit reserved about this. However, it's charging 14,5 volts on idle and 14,55 volts with half throttle.
You sir might just deserve a bunch of free pizzas, if it stays fine now I will be a happy man with some extra parts laying around, like a fully working stator assembly haha.
Question now, can I leave the brown wire out? The reverse light works and the stop switch works, seems there would be a reason for that wire to be there. Can it be disconnected without causing other problems down the line? Maybe the wisest thing to do is to find out where it grounds and fix it...