Here's what I did
I washed the pieces in water (room temp) with a little shampoo in it. I rinsed it off completely and dabbed it dry with a lint free cloth. I then placed it in a large tupperware to air dry with the lid slightly ajar.
After about a week, I gave it 2 light coats and 1 medium coat of Gunze Sangyo Mr. Surfacer 1000. It was the end of the can so that may be the problem.
I let it dry for a few days (3 or 4) and then sprayed it with tamiya semi-gloss black (inside) and saw the dots. I thought something was wrong with the paint so I sprayed the hood with gloss alum. Since it happened to the hood as well, i think it;s the Mr. Surfacer.