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 combine and shorten prayers at home before traveling?
It is impermissible to combine and shorten prayers at home before traveling because a person is called a traveler once he/she departs the borders of his/her country, and offering prayer that way was originally intended to exempt a traveler. And Allah Knows Best.
What is the ruling on having brotherly ties between a strange man and a strange woman, and is the former considered a Mahram (unmarriageable) to the latter?
Such a relation between a strange man and a strange woman is forbidden in Islam because it involves forbidding what Allah has allowed by marriage, and allowing what Allah has forbidden such as looking and the like. Such a relation doesn`t render any act lawful between them, thus they are forbidden to look at each other, have a Khulwah (seclusion), and travel together.
What is the best manner in distributing the meat of the Aqeeqah?
It is better to divide all of it as cooked meat amongst the poor and the needy. Dividing it into three portions is a Sunnah, but it is permissible to keep all of it provided that a portion, even a small one, is given to the poor and needy (one kilo for example).