If you own a dremel tool or even a die grinds, I would grind those places out to clean solid material, and then if they are not very large, I would mix up some peanut butter with either 1/4" or 1/2" cropped fiberglass mixed in the PB and fill them in. Then go over the area with either CSM or 1708 to finish it off, but also feather in so it isn't standing out so you will have a smooth flat surface on the outside hull.
As you work with polyester and fiberglass and PB, you will see how it can work for so any areas. You can control the mixtures to get thick putty like mixtures, or thin syrupy mixtures by adjusting the ingredients. The real key to working with polyester is mix things well before using the kicker MEKP. Because once that is added, it needs to be thoroughly mixed to make sure it is mixed with all the ingredients, and the clock starts ticking.
Looks like you're doing great work thus far. :thumb: