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.
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.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
I suffer from absentmindedness and constant worries during prayer, what should I do?
You should take refuge in Allah from the whispers of the devil and life worries. You should also seek Allah`s help and offer a lot of Istigfar (seeking the forgiveness of Allah). And Allah Knows Best.