What is the ruling on someone who perform their prayer after finishing it because they believe they missed a Rak'a, a prostration, or that they did not perform it correctly (thinking their prayer was invalid)?

How does a praying person prostrate?

All perfect praise be to Allah,The Lord of The Worlds                                                                                                                                                                        It is from Sunnah that he/she sits with both knees on the ground in order to prostrate, then hands, nose and forehead are placed on the same place. In addition, the toes have to touch the ground, and be directed towards the Qiblah (direction of Ka`bah) during prostration. And Allah Knows Best.

Is it permissible to pay the Fitr Zakah (obligatory charity) of Ramadan on behalf of a dead person?

The Fitr Zakah of Ramadhaan isn`t due on one who had passed away before the sunset of the last day of Ramadan. 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.