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 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 a guardian (Big brother) to unlawfully stop his sister from getting married?
If the guardian denies her right in getting married for an unlawful reason, she should go to court in order to settle that matter, and the guardian is considered sinful in this case.