Are phone conversations between the two sexes permissible if for consultation, and within the limits of good manners?
Such act is impermissible since it renders hearts corrupt, and could lead to forbidden attachment. Allah, The Almighty, Says (What means): "and follow not the footsteps of the devil." [Al-Baqarah/68].
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.
Is it permissible to offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?
It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.
Should the Zakah (obligatory charity) giver tell the poor recipient that this is the Zakah of his money?
No, he shouldn`t. But, the Zakah giver should make an intention in his heart that it is the Zakah of his money when paying it to the poor. And Allah Knows Best.