Is it permissible for a person, who vowed to offer two Rak`ahs(units of prayer) everyday for Allah`s sake, to do so after the Fajr(dawn) prayer?

In principle, a vow should be fulfilled as it was originally intended, and if its time lapses then, it should be fulfilled at any time because of the vow. Therefore, it is permissible to offer them after the Fajr prayer, and there is no prohibition in doing so. However, it is preferable for him to offer these two Rak`ahs at some other time to avoid the disagreement amongst the scholars in this regard.

Is it permissible for a woman to apply Kuhul (Halal eyeliner) and go out wearing it?

Kuhul is part of a woman`s adornment, and it is forbidden for her to show that to anyone other than a husband, or a Mahram (Unmarriageable kin).

Is it permissible to make up for missed fast after the beginning of the second half of the month of Sha`ban (the month before Ramadan)?

Yes, it is permissible, but one who had missed fasts should hasten to make up for them. As for the Hadith mentioned in this regard, the prohibition is for offering absolute voluntary fasting. And Allah Knows Best.

What is the ruling on performing voluntary prayers during official working hours?

All perfect praise be to Allah, The Lord of The Worlds, and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions

There is no harm if  there was break time during official working hours, but if not then it is impermissible. And Allah Knows Best.