I took a car from the Orphans' Fund Development Institution; is there usury (Riba) involved in this transaction?
If the Sharia's conditions were met, then there is no harm in this. And Allah The Exalted Knows Best.
Is it permissible to repeat the Istikhara (seeking guidance) prayer, and is it a condition that one should sleep after offering it?
All perfect praise be to Allah,The Lord of The Worlds Istikhara is offered once, but it is permissible to repeat it, and sleeping after offering it is not a condition for its validity. 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.
What is the ruling of Sharia on woman shaking hands with non-Mahram man?
All perfect praise be to Allah the Lord of the Worlds. May His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
The Messenger of Allah (PBUH) said: "It is better to be stabbed in the head than touch a woman to whom one isn`t related." [Transmitted by Al-Tabarani /Al-Mo`jam Al-Kabir, Hadith No.16880]. Accordingly, it is forbidden for men to shake hands with non-Mahram* woman. And Allah The Almighty Knows Best.
* The women/men that you are allowed to marry. It includes all women/men other than mahram (including cousins).