Is what happened to the deceased’s father—his heart stopping and then his brain activity returning after he was declared clinically dead two days prior to his passing—considered a miracle (karamah) from God for him? And is it permissible to recite the Quran, give charity, supplicate, and dedicate the reward thereof to him, or are there other deeds that can be done?

The deceased benefits from whatever the living dedicate to them of the reward for good deeds, supplication (du'a'), and charity (sadaqah). Charity and supplication are better than dedicating the reward of Qur'an recitation. It cannot be definitively asserted that a deceased person waking up after doctors have despaired is a miracle (karamah), and the greatest miracle is adherence to righteousness (istiqamah).