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).
Is it permissible for a mother to stop her daughter from marrying a respectable, God-fearing young man because he isn't college/university graduate?
It is impermissible to deny a woman her right in getting married except for a lawful reason, and problems can be solved through dialogue. However, she can file a suit in order for the judge to have a say in that regard.
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.
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.