Is washing the private part after urinating (Istinjaa`) a condition, and is it done with water and soap, or with water only?
Istinjaa` is obligatory for removing impurity, and it can be done with toilet paper, or a stone, or water. It is preferable to do Istinjaa` first with paper, or stone, or the like, then to wash the private part with water until making sure that the impurity has been removed. Using soap is not a condition, but there is no harm in doing so provided that it is washed off with water. It is also permissible to use either water, or paper if impurity is removed by any.
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 deal with the whispers of the devil with regard to ablution and purity?
Whispers in ablution are from the devil, and so you should take refuge in Allah from the devil`s evil suggestions that aim to distort the religion. Thus, once an organ is completely pure, don`t question its purity since having whispers doesn`t mean that the purity is invalid as it has already been established.
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.