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.
What is the ruling on praying behind a disliked Imam?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
It is mildly disliked (Makruh Tanzihan) for a man—other than the permanent designated Imam (Imam Ratib)—to lead people in prayer if the majority of them dislike him due to a religiously blameworthy reason (Amr Madhmum Shar‘an), such as associating with open sinners (Fussaq), for example. As for the followers who dislike him, the prayer behind him is not disliked for them. However, if less than the majority dislike him, or if the majority dislike him for a reason that is not religiously blameworthy, then his leading the prayer is not disliked. And Allah the Exalted knows best.
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`m a pious Muslim woman, but my husband isn`t, what should I do?
You should exercise patience, make supplication that Allah guides him to the straight path, and keep advising him kindly.