A man has raped a woman and she gave birth to a baby boy. To whom should that baby be attributed?

Is permissible to include a will requesting that a Holy Qur'an buried along with me?

It is not permissible to include a will requesting that a Quran be buried with the deceased in their grave. This is because the body of the deceased typically decomposes and may release impure substances, and it is not allowed to expose the Quran to impurity. Intentionally desecrating the Quran is an act of disbelief. Instead, read the Quran during your lifetime, as it will benefit you after death. And Allah Knows Best.

What should one who made an intention, at night, to make up for a missed fasting day, but broke his fast on the next day?

One who started making up a missed fasting day, then broke his/her fast without a legitimate reason is considered sinful, and is only obliged to make up for the missed fasting days. And Allah Knows Best.

What should a person, who doubts the validity of his Wudu, or over performs it, do?

One who doubts the validity of his/her Wudu while performing it should redo it until he/she is certain of having attained purity. But, if doubt was after having performed Wudu, then he/she should not pay attention to that as doubt after the end of an act of worship does not count. This is of course in case doubt was within the reasonable limits since once it goes beyond that, it becomes a whispering of the Shaytaan (devil) which he/she should ignore as the Wudu is valid.