When you have a side apart and are ready to put on the new rotor, slip on a pair of nitrile gloves, have a supply of clean blue shop paper towels handy, spray a blue towel with brake cleaner and wipe on the pad contact surfaces. Might want to start with the back so you can see how well the nice gray coating they applied to the hats, edges, and vents will deal with the brake cleaner. You don't want to remove the gray stuff, it keeps the brakes pretty. If the protective stuff they applied to the shiny friction surfaces to prevent rust on the shelves is over the gray stuff, I wouldn't worry about it unless it's some nasty greasy stuff that will attract dirt. If it's cosmoline, I'd prefer it not to be on there, but it can be tough stuff to remove and you might damage the nice gray coat trying to get it off.
Really, just use your good judgement, just be sure to wipe down the friction surfaces with brake cleaner until the wetted towels come up clean. Then put it all back together, take care to keep the brake fluid off or clean things off again when it's all done (this is why it would be good to know how well the gray coat that you want to keep deals with brake cleaner because it's sometimes easier to just spray the rotors and let them drip dry when they're installed....you want to avoid that if it'll end up making things ugly and you don't want to be disolving more crap that drips onto the rotors, leading to more cleanup, and possibly ugly rotors).
Some strategic use of aluminum foil can keep the brake fluid and gunk off the rotors while you patch everything up. Just don't let parts of a foil sheet that might touch dirt and grime touch the rotor friction surface or the pads.
Again, just common sense, your good judgement, and some **** retentive/obsessive compulsiveness towards keeping the friction surfaces clean. Pretend you have a hand washing OCD and the rotors and pads are your hands and everything else is covered in germs.
