What should I do about the many intrusive thoughts concerning Allah - exalted be He - such as "Who is He? And why did He create us? And why did He create us when we disobey Him, and He is free of need of us and our worship?", which choke me when I recite and ponder the Quran, and make me feel hypocrisy and atheism, and fear of disbelieving in Allah?

You must turn away from these whisperings (waswas) and pay them no mind. Say: "I believe in Allah" whenever a whispering occurs, then seek refuge in Allah from Satan, and stop these thoughts. These whisperings will not harm you as long as you dislike them, and you will be rewarded for your struggle against them. Abandon those thoughts that Satan casts into your heart, and strive to rid yourself of them.