First, great job on taking such good care of your teeth. More and more, we are learning that good oral hygiene can prevent a multitude of illnesses later in life, including heart disease (among others). Next, it is difficult to tell from your question exactly what it might be that is going on inside of your mouth. Many different diseases and minor issues can occur in this area, and it is important to see a doctor
in person so that they can feel and see these spots in person.
That being said, it is quite possible that what you are seeing are Fordyce granules, which are tiny glands that show up on the inside of your mouth and are painless, slightly yellow, and absolutely harmless. They could be presenting in the way that you are describing, but, again, it is hard to say without a picture or at least more information. Canker sores, or aphthous ulcers, are also common in this area, but are usually quite annoyingly painful.
Now, it is important to note that these spots could be something more ominous, and you should see a physician to have them evaluated. You should be especially prompt if you have a smoking history or family history of any unusual diseases or head and neck cancer. While it is unlikely that these are anything serious, it is still important to see a physician.