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 it permissible to give Zakah (obligatory charity) to one`s poor sister, or brother?

It is permissible for one to give the Zakah to his poor sister, or brother if providing for them isn`t due on him, and the sister doesn`t receive sufficient provision from whomever that is due on. And Allah Knows Best.

Is it permissible to single out Fridays, Saturdays, and Sundays to make up for missed fasting without fasting a day before ,or after each ?

Yes, it is permissible to make up for missed fasting during the aforesaid days, and it is also valid to offer non-obligatory and vowed fasting as well. However, fasting a day before or after each isn`t obligatory. And Allah Knows Best.

What is the ruling on combining prayers at the Musala (Place for prayer) of a shopping center because of heavy rain, knowing that some people come from outside that center?

Praise be to Allah, the Lord of the Worlds.

If there is hardship in going back to that Musala at the time of Asr or Isha` prayers, then it is permissible to combine prayers in twos only (Duhr with Asr and Maghrib with Isha`). Kindly consider calling us. And Allah Knows Best.