How can one atone for a cry of pain directed at his mother before her death, and remove the effect of this painful memory from himself, despite his supplications for her with mercy and forgiveness and his performance of good deeds in her name?

The apparent state of your mother is that she died pleased with you, due to the intensity of your remorse and your eagerness to please her, and because she embraced you to her chest on the night of her death. So trust in Allah and have a good opinion of Him. You must repent from smoking and quit it. It is not permissible for you to say in your supplication: "I seek refuge in Allah and in you (plural)."