I think if I connect another power connector from the PSU than the "case fan only" connector to the fan control, I can fix the fan control problem. I think you are right about the fan control just not adjusting the amount of voltage properly, to run the fans properly.
As for the PSU, I guess I'll just have to mount it upside down, but I'm worried about the ventilation. Maybe I can make some ventilation holes on top of the case (which would ruin it). There is some space, I can almost fit my hand in there, if I lay it flat, but still, I dont really think its good enough personally.
What do you suggest? Should I just mount it upside down?