Does the time of Fajr (dawn) prayer start after the first Athaan (call for prayer), or the second one?
All perfect praise be to Allah,The Lord of The Worlds The time of Fajr prayer starts after the second Adhan. And Allah Knows Best.
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.
What is the ruling on making up missed fasts from many years?
A Muslim must make up for any missed fasts, as they are a debt owed to Allah. The Prophet ﷺ said:
"The debt owed to Allah is more deserving of being fulfilled." [Narrated by Muslim]
Whoever has missed fasts must make them up as long as they are alive and capable of fasting.
Is it valid to perform the obligatory prayer while sitting?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
Standing (Al-Qiyam) while having the ability to do so is one of the pillars (Arkan) of the prayer; the obligatory (Faridah) prayer is not valid without it. However, whoever is unable to stand may pray sitting down. As for voluntary (Nafilah) prayers, it is permissible to pray them sitting even if one is able to stand, but the one sitting receives half the reward of the one who prays standing. And Allah the Exalted knows best.