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.
Does the fast become invalid if water from rinsing the mouth reaches the stomach while performing ablution?
If water reaches the stomach without the fasting person exceeding normal rinsing or being excessive, their fast remains valid.
However, if they exceed the normal practice or exaggerate in rinsing, causing water to enter the stomach, their fast is invalid.
This is because excessiveness in rinsing is prohibited for a fasting person, as the Prophetﷺ said: "Exaggerate inhaling water during ablution, except when you are fasting." [Narrated by the Four Imams]
Transgression (Ta‘addi) refers to rinsing the mouth more than three times, while exaggeration (Mubalaghah) includes gargling, drawing water deep into the nasal passages, or filling the mouth with water in an unusual manner.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
What should a person who doubted having missed a pillar of prayer do?
All praise be to Allah, The Lord of The Worlds. The prayer of one who doubts having missed one of its pillars is valid, and nothing is due on him/her since having a doubt after offering the act of worship doesn`t undermine its validity. And Allah Knows Best.