Steve,
There is a simple answer at least to the ghost runs. That is where the painter got a little happy with the gun and laid too much paint in that spot and got some serious runs in the paint. They went back later and lightly sanded the runs out using a flat block, plenty of fresh water, and super fine sand paper. After they are blocked flush with the car, they hit them with the buffer. The darker the color the more obvious they may appear to be. What happens is the paint still reacts and or shrinks a little over time and the area where the run is will re-appear. There is nothing you can do about it, other than repaint. What you have is a distortion in the finish (usually the clear coat) not unlike that of a lense change in your glasses, or camera. Although it is clear, there is just enough difference in the lay up of the material to bounce light different and leave the illusion of a run that is no longer there.
Hope that answers it for you! I would also bet that somebody touched the car while it was in primer/sealer, or just before spraying and the hand print was not chemically cleaned off. Therefore the paint reactact to the oils left in the hand print like a forensic detectives dream come true..
This is why I will avoid all mechanical work possible before painting, I won't let anybody touch a car I have in primer, and I will wash it two or three times with dishwashing grease fighting detergent, then two or three chemical wipe baths before topcoating.