Mine has some paint starting to peel as well and also paint missing around the spark plugs (almost like it had been slowly burned off over the years). It's not a matter of cleaning it or brightening it, it needs the paint touched up. Mine's the factory original wrinkle black, and I'd sure like to know what I could use to touch it up too. It would need more than just a touch up pen I think. Something I could spray with an air brush would work.
H-D sells the wrinkle black in spray cans. I've done a bunch of top ends with good results. The main thing is the parts to be painted need to be CLEAN ! I use a 1500 watt space heater to get the paint to wrinkle up and cure. Just running the engine doesn't get the paint to wrinkle evenly.