Does an internal examination require ghusl?
Ghusl isn't required for making internal examination; however, it invalidates one's fasting. And Allah Knows Best.
Is it permissible to fast on behalf of the dead who died owing missed fast to make up?
His relative should fast on his behalf, and it is permissible for the guardians to give permission to non-relatives of the dead to fast on his behalf as well. 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.
The supplication: "O Allah, we do not ask You to avert the decree, but we ask You for kindness in it." Is this Supplication Halal or Haram?
We are obliged to supplicate Allah, so when supplicating we comply with Allah's Ordainments, and making supplications that are reported in the authentic texts is better. And Allah Knows Best.