The supplication: "O Allah, we do not ask You to avert the decree, but we ask You for kindness in it." Is this Supplication Halal or Haram?

We are obliged to supplicate Allah, so when supplicating we comply with Allah's Ordainments, and making supplications that are reported in the authentic texts is better. 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.

Is wearing a cap permissible for boys, or girls?

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

In principle, anything is permissible sol long as there is no Sharia evidence prohibiting it, thus wearing the cap by boys is permissible as long as it isn`t done in imitation of the disbelievers. Moreover, a Muslim woman should avoid all that which attracts the attention of men because whatever leads to the forbidden is forbidden. And Allah Knows Best.

What is the ruling on loudly sending prayers on the Prophet (PBUH ) after the call for prayer Athaan?

All perfect praise be to Allah, The Lord of The Worlds                                                                                                                                                            Sending prayers on the Prophet after Athaan is a Sunnah for the Mou`zen (caller for prayer ) and the hearer. However, there is no harm in doing it loudly after the end of Athaan, but sometimes, it shouldn`t so that people wouldn`t think that it is an integral part of the Athaan. And Allah Knows Best.