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.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
What is the ruling on the ablution of one who cuts his nails, and is it permissible to cut them before the ritual bath for major impurity (janabah)?
Cutting nails does not invalidate ablution, and it is permissible to cut them before the ritual bath for major impurity. And Allah the Almighty knows best.
Is it permissible to pay the Zakah (obligatory charity) for settling the debt of a deceased relative?
It is impermissible to pay the Zakah for settling the debt of the deceased since Zakah is paid to eligible recipients who are alive. As for the debts of the deceased, they are to be settled from the estate before dividing it amongst the heirs, but if the deceased didn`t leave an estate, then it is desirable for his/her heirs to settle those debts if they can afford them. And Allah Knows Best.