Derek -- on the headliner smudges -- try a can of Cyclo's Max Clean. The stuff is excellent on anything covered in mouse fuzz; lifts the dirt right out, doesn't even need to be scrubbed to look like new.
The three black clips should be installed in the headliner board before sticking it in the car -- the pictures implicate that they were fitted to the board with them snapped to the roof, which I think would be impossible.
best, whit