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.
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 Salah (prayer) on behalf of the sick who is on his/her death bed, and is incapable of offering it?
It`s impermissible to offer Salah on behalf of the sick, or the dead.
Is it permissible for us to sever ties of kinship if our blood-relatives` gatherings/meetings involve acts of sin?
Observing kinship ties is obligatory, and paying your blood-relatives a visit causing their sinful acts to be hindered , then you should do so. However, if their sinful acts continue while you are at their gathering and they didn't respond positively, then observing kinship ties via telephone and the like will suffice in this case. And Allah Knows