How can one rid their heart of hypocrisy and doubts towards Allah, His Messenger (peace be upon him), and the Qur'an, which arose from their persistence in sins and lack of obedience, despite their repeated attempts at repentance that failed to eliminate these doctrinal sins?

As long as a person desires to repent, they are not guilty of major hypocrisy. They must immediately repent of their sins, and know that Allah is All-Forgiving, All-Merciful, accepting the repentance of the penitent, no matter how great their sin. Therefore, they must be sincere in their repentance and turn to Allah with devotion. If they return to sin, they should return to repentance and not despair. They must also take the necessary measures to protect themselves from repeating the sin, such as supplication (dua), remembrance of Allah (dhikr), keeping good company, avoiding the causes of sin, reflecting on Allah's Names and Attributes, and increasing good deeds.