What is the ruling on intermittent spots of blood that are not confirmed to be menstruation, and must one make up the prayers missed due to abstaining from them based on the assumption that they were the beginning of menstruation, which was not certain?

The majority opinion is that the minimum duration for menstruation is one day and one night. If what you are seeing are merely spots, with complete dryness in the area, such that if you were to insert something, it would come out untainted by blood, then this is not menstruation, and you should pray with it. You were mistaken in abandoning prayer due to these spots, and you must make up the missed prayers.