Does using a wet miswak while fasting break the fast?

Is it permissible for a praying person to make supplication in each Sajdah (a prostration) of obligatory prayer?

It is permissible for a praying person, whether praying individually, or in congregation, to make supplication during Sujood (prostration) in obligatory, or voluntary prayers. However, it is disliked for the Imam to do so since he is required to spare the prayer performers any sort of hardship, unless he is leading a certain group who don`t mind him extending the prayer.

Is it permissible to give multiple mudds (portions) of fidyah to a single person?

Yes, it is permissible to give multiple mudd of fidyah to a single person, because each day of fasting is considered an independent act of worship.

What is the ruling on water present on the floor of a toilet/bathroom?

The default ruling is the purity of this water present on the bathroom floor. If one is certain or strongly suspects its impurity, then one washes whatever part of the body or clothing this impure water has touched. If one doubts its impurity, the default is purity, and we do not rule it impure based on mere doubt. And Allah the Almighty knows best.