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 incumbent on the fiancée to obey her fiancé?
When the woman settles in her husband`s house, it is incumbent on him to provide for her and it is incumbent on her to obey him. Before that, and if the marriage contract had been concluded, then she is lawfully his wife and thus she should abide by custom in treating him, but if the marriage contract hadn`t been concluded, then she should treat him as a non-Mahram (Marriageable).
I prayed all the obligatory prayers in congregation, but after finishing the `Isha prayer, I remembered that I had forgotten to pray Dhuhr. What should I do, and is my prayer invalid?
Your prayers are valid, but you must make up the Dhuhr prayer as soon as you remember it, based on the saying of the Prophet (peace be upon him): "Whoever forgets a prayer must pray it as soon as they remember it; there is no expiation for it except this." [Muslim]. And Allah knows best
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.