What is the ruling on smoking?

All Perfect Praise is due to Allah, The Lord of The Worlds

Smoking is forbidden (Haram) since it is harmful to one`s health as confirmed by trustful physicians, and Islam has forbidden taking anything that causes harm. The Prophet (PBUH) said: "There should be neither harm nor reciprocated harm." [Ibn Majah and Ahmad]. And Allah Knows Best.

I work in a government institution that gives an additional three dinars per hour I work. The manager combines students into a single session because attendance is low, and the material taught to all groups is the same. I am paid for two hours, although I actually taught only one session, noting that my transportation costs one and a half dinars. What is the ruling?

The only amount you are permitted to take/have is for one hour work. And Allah Knows Best.

Does Istigfar (Asking Allah for forgiveness) between the first and the second part of Friday prayer`s sermon render the prayer invalid?

Talking during Friday prayer`s sermon is disliked, but there is no harm in offering Istigfar between the two parts of the sermon, and it doesn`t invalidate the prayer as it is actually from Sunnah. 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.