My MK 5 was covered in specs of contaminates most of them orange. After a bit of research found them to be called rail dust.
Basically once your car has been completed and parked up ready to be shipped off around the world any airborn sh!t floating around sticks to nice fresh soft paint. If its metal it rust and thats the orange colour. I think the name rail dust came from the USA as probably a lot of the cars got transported by rail for obvious reasons so they were parked next to the railway line.
These marks should easily come off with the appropriate type of clay used by a pro detailer as its easy to marr the paintwork if you dont really know what your doing.
I would be going to a detailer of my own choice and then billling VW.
As for the stains i cant help you with that but again a pro detailer would be able to remove it if possible. The dealer paint protection stuff is garbage and not worth the money.
As for rejecting the car i dont know the law but i thik you have to give them the chance to put things right first even if it means a total respray.
Good luck.
