How can one get rid of religious whisperings (waswas) and doubts, and must missed prayers be made up, and is doubting the pillars of faith considered disbelief (kufr), and what is the way to remove hardness of heart and feel the presence of God?

Whoever confronts the شبهات (doubts/misconceptions) of atheists before arming himself with religious knowledge has erred. These intrusive thoughts (وساوس) do not make him an infidel (كافر) or a sinner (آثم). He is advised to supplicate (دعاء), consult a trustworthy psychiatrist, abandon the intrusive thoughts about purity (الطهارة) and other matters, and make up for missed prayers.