Is it permissible for a person who has to make up for missed fasts to fast six days of Shawwal (the month directly after Ramadan) before making up for the missed fasts?
Yes, it is permissible for him/her to do so, but it is better that they make up for missed fasts first. And Allah Knows Best.
Is washing the private part after urinating (Istinjaa`) a condition, and is it done with water and soap, or with water only?
Istinjaa` is obligatory for removing impurity, and it can be done with toilet paper, or a stone, or water. It is preferable to do Istinjaa` first with paper, or stone, or the like, then to wash the private part with water until making sure that the impurity has been removed. Using soap is not a condition, but there is no harm in doing so provided that it is washed off with water. It is also permissible to use either water, or paper if impurity is removed by any.
What is the ruling on memorizing the Quran during menstruation, knowing that I do not read directly from the Quran but from a paper or from my phone?
It is not permissible to memorize the Quran during menstruation because memorization requires repetition, and a menstruating woman cannot touch the physical pages of the Quran. Similarly, if the Quranic verses appear on the screen of the phone, it is considered like touching the Quran. And Allah Knows Best.
How many Rak`ahs (unit of prayer) are offered in Witr prayer?
All perfect praise be to Allah, The Lord of The Worlds Witr (an odd number prayer performed between Isha`a and Fajr) is offered with a minimum of one Rak`ah, and a maximum of eleven, but offering three Rak`ahs is the minimum of its complete form. And Allah Knows Best.