Oil in the intercooler pipe work would be from the recirculation of blow by gasses, these enter the intake pipe through the breathers ontop of the cam covers and the PCV ( Positive Crankcase Ventilation) valve and into the intake pipe just after the AFM. Only way to stop it is to fit a properly baffled catch can set up.
As for the rough running, low boost and black smoke, i'd be checking all the clamps and hoses on you intercooler pipes. Sounds to me like there is a boost leak.