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 someone who eats or drinks assuming that the night is still present, then realizes that dawn has broken?
Whoever eats or drinks assuming that the night is still present, then later discovers that dawn has broken, must refrain from eating and drinking for the rest of the day out of respect for the sacred month. However, they must make up that day after Ramadan, and there is no sin upon them.
What is the ruling on performing istinja' before every ablution?
Istinja' is not from the conditions for the validity of ablution. It is only obligatory for prayer when there is impurity from urine or stool on the private part, or if there is fear of the impurity spreading to the body or clothing. And Allah the Almighty knows best.
Is it permissible to slaughter one animal as a sacrifice and an Aqeeqah (the sheep slaughtered on the seventh day from the child`s birth)?
It is impermissible to do so since each of them is slaughtered for a different reason.