Does the time of Fajr (dawn) prayer start after the first Athaan (call for prayer), or the second one?
All perfect praise be to Allah,The Lord of The Worlds The time of Fajr prayer starts after the second Adhan. And Allah Knows Best.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
What is the ruling on someone who prays but does not fast, without a valid excuse?
Fasting is one of the pillars of Islam, and a Muslim's faith is incomplete if they neglect the obligation of fasting while being physically capable of observing it.
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.