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.

What should a praying person who doubts having offered one, or two prostrations in the third Rakah (unit of prayer) do?

Whoever has doubts about their prayer should consider what is less i.e. the above person should offer another Sajda (prostration) and complete his/her prayer, then offer Sujood As-Sahw (prostration of forgetfulness). 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 staring at the Holy Ka'abah?

All perfecy praise be to Allah, The Lord of The Worlds and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions.

Staring/looking at the Holy Ka'abah is an act of worship even if this took place while performing a prayer, since Al-Baihaqee stated that the Prophet (PBUH) said: " Staring at the Holy Ka'abah is an act of devotion." [Sho'aab Al-Imaan]. And Allah Knows Best.