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.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
If a woman becomes pure from menstruation shortly after Fajr in Ramadan, what is required of her?
If a woman becomes pure (from menstrual period) after Fajr, even shortly after, it is recommended (but not obligatory) for her to refrain from eating and drinking for the rest of the day. However, she must make up for that day after Ramadan.
She will be rewarded for both refraining from eating (imsak) and making up the fast (qada) since she was menstruating for part of the day.