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.
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)?
If he was sure that his prayer is void then reperforming it is an obligation along with figuring out the reason of invalidity so long as this wasn't out of uncertainty. And Allah Knows Best.
How are gaps filled during congregational prayer?
A praying person is allowed to take two steps in order to fill the gap in the row ahead. If the distance was long and requires much movement, then it is impermissible for one to move to fill it because much consecutive movement (three movements) during prayer invalidates it.
Is a Muslim is Permitted to Pray Wearing Shoes?
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 There is no harm for a Muslim to pray wearing shoes or slippers so long as they are pure, since a man asked Anas Ibn Malik: "Did the Prophet (PBUH) use to offer the prayers with his shoes on?" He said: "Yes." Moreover, Ibn Rajab (May Allah have mercy on his soul) said: "Performing prayer wearing slippers/shoes is permissible according the majority of the Muslim scholars." [Fatih Al-Bary,vol.2/pp.274]. And Allah Knows Best.