Would a charitable act of building a well with ill-gotten money alleviate some burden from the deceased from whom this money was inherited?

Unlawful wealth is spent to get rid of it, not as charity. We do not believe that your father will benefit from your disposal of it, as long as he did not repent from it during his lifetime. However, the repercussions of its continued existence might cease for him. If the wealth belongs to other people, his liability is cleared by returning it to its owners if they are known, or by giving it as charity on their behalf if they are unknown. If you give charity on his behalf from lawful money, he will benefit, Allah willing. Likewise, he will benefit from your supplications and seeking forgiveness for him.