Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
What is the ruling on using a miswak (tooth-stick) during the day in Ramadan?
It is permissible to use a miswak before noon while fasting. However, according to the Shafi'i school, it is disliked (makruh) after noon in order to preserve the natural effect of fasting in the mouth, as the Prophetﷺ said in authentic hadith:
"The breath of a fasting person is more pleasant to Allah than the fragrance of musk."
How many Rak`ahs (unit of prayer) are offered in Witr prayer?
All perfect praise be to Allah, The Lord of The Worlds Witr (an odd number prayer performed between Isha`a and Fajr) is offered with a minimum of one Rak`ah, and a maximum of eleven, but offering three Rak`ahs is the minimum of its complete form. And Allah Knows Best.
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.