This probably has been done before but I'll mention it for any other perfectionist types. Touching up dings on my paneling with putty was not quite good enough. Even the nail hole putty can stand out for some OCD types. Stain is not going to be absorbed, or course. At Walmart in their arts and crafts area you will find enamels and acrylic paints in inexpensive small containers. You may need to mix them. Take a very small model type paint brush and dab away at these areas. They will largely disappear if you get your paint color right. (I know - scratches may not cover as well as minor dings) Frank
I had good results with colored pencils as well on a travel trailer that was essentially made of sawdust and paper, and was far too easily scarred.
The large Joanns and Micheals craft stores have paint sections that stock hundreds of various colors paints, in small bottles.
My wife was able to pick an exact match to our 2003's white paneling from a selection of dozens of whites.
Take a sample with you for the best results.
Larry