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.
What is the difference between Tahajjud prayer and night prayer, and do they have a particular Witr prayer other than that of Isha (evening prayer)?
Tahajjud and Qiyam-Al-Lail (night prayer) are two words for the same meaning which is offering voluntary prayer at night after sunset, but before dawn break. However, Tahajjud is offered after waking up; whereas, Qiyam-Al-Lail is permissible before sleeping, or after it. Therefore, every Tahajjud is a Qiyam, but not every Qiyam is a Tahajjud. Moreover, there is no specified Witr for both of them, but Witr after Isha is by itself the Witr of Qiyam, and it is a Sunnah to postpone it until after Qiyam if the worshiper thought that he was most probably going to wake up in order to offer it, but if he wasn`t sure of waking up, then he is at liberty to offer it before going to bed as was reported in the Prophet`s Hadith.
Does bleeding from the body, such as from wounds, invalidate ablution?
Bleeding doesn't invalidate person's ablution. And Allah Knows Best.
Is prayer nullified by having thoughts while performing it?
Prayer isn`t nullified by having thoughts while performing it, provided that the praying person offers all of its pillars and meets all of its conditions. However, the reward decreases significantly in the absence of reverence since a praying person is rewarded according to the attentiveness of his/her heart during prayer.
