Is it permissible for a wife to refuse to go to bed with her husband (for sexual intercourse)?
It isn`t permissible for her to do so unless for a sound reason.
What do you say about someone who stays up all night on Laylat al-Qadr but misses Fajr prayer?
Such a person has deprived themselves of a great reward. Performing obligatory acts is more beloved to Allah than voluntary acts. Fajr prayer is an obligation, and performing it in congregation is equivalent to worshiping for the entire night. So how can someone neglect it while striving for voluntary prayers?!
What is the ruling on someone who eats or drinks thinking that the night is still present, then realizes that dawn has broken?
Whoever eats or drinks thinking 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 istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.