How can one get rid of intrusive thoughts and doubts that arise in the mind concerning religious matters, and what are the books that address such questions and strengthen faith, bearing in mind that the Holy Quran may be difficult to fully comprehend?

The state you described is an effect of waswasah (whispers/obsessive thoughts), not doubt. The sign of this is your dislike of these thoughts, and your fear and aversion towards them. However, for one to follow waswasah, speak about it, spread it, and reach a level of doubt that shakes the pillars of certainty and contradicts Tawhid (definition) (monotheism) — that is when one's faith is truly feared for. And the love of Allah and His Messenger is a condition for faith; it is not valid without it.