What is the ruling on entering the toilet with something containing the remembrance of Allah?
It is disliked to bring into the toilet anything containing a reminder of Allah, such as the Quran or a sacred name (like the name of Allah, Muhammad, etc.). If one does that, etiquette dictates that he conceal it so it is not visible while entering the toilet, either by cupping his hands over it, putting it in his pocket, or inside his shirt if it is a necklace or ring. And Allah the Almighty knows best.
Is it permissible to make ablution without answering the call of nature after waking up?
Washing front and back openings (Istinjaa`) is not a condition for the validity of ablution because it is done to remove Najaasah (impurity), thus if there is no Najaasah, there is no need for that, and then it is permissible to make ablution without answering the call of nature. However, prayer is invalidated if there is Najaasah on the anus ,or the front opening, so it (Najaasah) must be removed for the prayer to become valid, and not the ablution.
What is the ruling on one who doubts washing a limb before or after finishing ablution?
If a person performing ablution doubts leaving the washing of a limb from the limbs of ablution during his ablution, he must repeat washing that limb and wash what comes after it. If he doubts leaving the washing of a limb after finishing the ablution, there is nothing upon him. And Allah the Almighty knows best.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.