Is it permissible for one to shake hands with his uncle`s daughter?
No, it isn`t because he is a non-Mahram (Marriageable) to her.
Is it permissible to make ablution without answering the call of nature after waking up?
Washing front and back openings (Istinjaa`) is not a condition for the validity of ablution because it is done to remove Najaasah (impurity), thus if there is no Najaasah, there is no need for that, and then it is permissible to make ablution without answering the call of nature. However, prayer is invalidated if there is Najaasah on the anus ,or the front opening, so it (Najaasah) must be removed for the prayer to become valid, and not the ablution.
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.
What is the ruling on eating or drinking during the second Adhan?
It is not permissible to eat or drink during the second Adhan because it announces the break of dawn and the obligation to start fasting. Allah Almighty says {what means}:"and eat and drink until you can discern the white streak of dawn against the blackness of night." [Al-Baqarah/187].
Whoever eats or drinks during this time invalidates their fast, and they must refrain from eating for the rest of the day and make up for the missed fast later.