While I did not paint an original, I did make my own and painted it to match my restored Gold Crown I. If you do decide to paint, use a Door and Trim or Cabinet Urethane Enamel as it will offer a better finish and dry harder than latex wall paint.
I clean the balls before every session in my ball cleaner using a mixture of 8oz 91% Isopropyl Alcohol with 2 tablespoons of Aramith Ball Cleaner. The balls come out clean, shiny, but not slick. Very much a "fresh out of the box" feel.
With all the work I put into my table, I don't think I'd sell it and start over. I suppose I could do it all again but I'd rather not if I didn't have to.
The red marks on the cue ball are obviously red chalk marks. The spots on the balls appear to be from pocket liners. What kind of table are you playing on and what are the pocket liners made from? What do you use to clean the balls?