Is the two Raka's after Friday Prayer an act of Sunna?
Performing Two prostrations after the call of Friday's Athan is an act of Sunna, since Al-Bukhari stated in his Sahih: (The chapter of praying before and after Friday's prayer). This indicates that he mentions Friday's prayer exactly as the Duhr prayer (Afternoon prayer) as regards praying before and after the call of Athan. And Allah Knows Best.
Is it permissible to listen to chants praising the Prophet if accompanied by musical instruments?
If singing, or chanting in praise of the Prophet was accompanied by a forbidden musical instrument, then it is forbidden.
Is Making up Missed Obligatory Prayers an Obligation?
All perfect praise be to Allah, The Lord of The Worlds, and may His peace and blessings be upon our Prophet Muhammad and upon all of his family and companions.
Missed obligatory prayer/prayers is a debt upon Muslim and making it up is an obligation, since the Prophet (PBUH) said: "pay the debt due to God, for it is the one which most deserves to be paid." [Agreed upon]. And Allah Knows Best.
What is the ruling on visiting a deceased's grave and supplicating Allah for him by his wife? Is the reward of reciting verses of the Holy Qur'an reaches the deceased?
There is no harm on visiting graveyard by woman with the intention of piety so long as they are dressed in accordance to the Islamic teachings. We ask Allah, The Almighty that the reward of reciting the Holy Qur'an on dedicated to the deceased reaches him. And Allah Knows Best.