I've used metal cleaner / wax (Mcguires metal cleaner) on the primary cover, and of course, I got some of the cleaner / wax on the black powder coat on the engine. I've tried a wet toothbrush, dry toothbrush, but it doesn't want to come off. Anyone have any suggestions on how to get this off?

 

You could try lighter fuel followed by a detergent (lighter fuel also branded Cleanart)

 

Some metal cleaners have an acidic reaction to metal, so that it can remove oxidation. Could have stained the wrinkle paint maybe. If it isn't coming off with a brush, then I'd try consealing it with silicone spray. Any brand will do really, as long as it is silicone based.

My bike engine was covered in dried wax from the previous owner. Nothing touched it, until I sprayed it down liberally with Pledge. Pledge loosened all the dry wax residue, with a soft bristled brush, and very little effort.

After that, I was told by some to use silicone spray. I will use either now, depending on what I have laying around. To me, they both seemed to give the same results, when I used them. I even spray the engine black with Pledge or silicone, while it is warm.