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 to offer prayer at home, or should it be offered in the mosque?
All perfect praise be to Allah, The Lord of The Worlds. It isn`t preferable for the man to pray at home as praying in the mosque is twenty seven times more rewarding. Therefore, this should motivate him to offer prayers in the mosque. And Allah Knows Best.
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.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.