What is the way to overcome the intrusive thoughts that prevent one from embracing Islam, despite being convinced of it as a religion?

You have traversed a difficult valley when you re-examined the religion you grew up with. Satan strives hard to turn people away from guidance by clinging to their ancestral traditions without proof. Your transition to atheism was a painful and dark experience, but your courage pushed you to seek the truth that combines meaning with the soundness of rational foundations. The moment of emotional resistance you are experiencing is natural, for a rational mind is one that blends logic with emotions. The voice saying, "Do not abandon the religion of your forefathers," is a satanic whisper that hinders guidance, as Allah warned in the Quran. The religion of your forefathers is false and meaningless. To rid yourself of this whisper, you must disobey it and flee to Allah, clinging to the most trustworthy handhold: "There is no god but Allah, Muhammad is the Messenger of Allah," and seek refuge with the Lord of mankind from the evil of the slinking whisperer. And just as Ibrahim (peace be upon him) did, you must break this negative voice with the voice of wisdom and rationality. The merits of Islam lie in its combination of sound rational foundations and integrated emotional aspects, for it answers the great questions of existence with a comprehensive value system. What remains for you on your journey is to pronounce the Two Testimonies, so that you may have been saved twice: from the polytheism of the Trinity, and from the futility of atheism.