How should I be kind to my atheist father?

Allah, The Exalted, has decreed and ordained his slaves to be kind with parents, even if they are polytheists, by honoring and obeying them in all that isn`t sinful, so that they might love Islam and embrace it as a result.

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.

Should Al-Basmalah (i.e. saying Bismillaaahi Ar-Rahmaani Ar-Raheemi) be recited after Takbeerat Al-Ihram (saying Allahuakbar) which marks the beginning of prayer?

All perfect praise be to Allah,The Lord of The Worlds                                                                                                                                                                        A praying person is obliged to recite Al-Basmalah at the beginning of Chapter Al-Faatihah, and in every Rak`ah (unit of prayer) because it is a verse of it. And Allah Knows Best.

Is wearing a cap permissible for boys, or girls?

All Perfect Praise is due to Allah, The Lord of The Worlds.

In principle, anything is permissible sol long as there is no Sharia evidence prohibiting it, thus wearing the cap by boys is permissible as long as it isn`t done in imitation of the disbelievers. Moreover, a Muslim woman should avoid all that which attracts the attention of men because whatever leads to the forbidden is forbidden. And Allah Knows Best.