Is it permissible for a person to sever ties with his sister because her husband had quit prayer and done him harm?

A sister is a blood-relative and maintaining blood-relations is obligatory in Islam. As regards her husband, he should be invited to the way of Allah with wisdom and beautiful preaching.

If the menses lasted for over than 9 to 10 days, considered menstruation?

If the duration of the bleeding does not exceed fifteen days, it is all considered menstruation, even if the usual pattern changes.

Does the deceased hear the supplications or recitations of those visiting his/her grave? And does making constant supplications for the deceased who didn`t adhere to performing the prescribed prayers ameliorate his/her affliction?

Praise be to Allah the Lord of the Worlds.

In principle, the dead hear the living since it has been rigorously authenticated that the Prophet (PBUH) ordered the bodies of the idolaters slain in the Battle of Badr to be buried. He then approached them and called them one by one and said: "Have you found what your Lord promised to be true for we have found what our Lord promised us to be true." Umar asked him: "O messenger of God! Why do you speak to lifeless bodies?" The Prophet (PBUH) replied: "By the One Who has sent me with the truth! You do not hear my words better than they do except that they cannot respond." [Agreed upon].

However, not all the deceased are in the same situation because Allah The Almighty Knows: "Before them is a Partition till the Day they are raised up." [Al-Mu`minun/100]. Moreover, supplication reaches the deceased. And Allah Knows Best..

Where should a woman who is led by her husband in prayer stand?

All perfect praise be to Allah The Lord of The Worlds                                                                                                                                                                          It is from Sunnah (Prophetic tradition) that she stands behind him. And Allah Knows Best.