How should I deal with the whispers of the devil with regard to ablution and purity?

Whispers in ablution are from the devil, and so you should take refuge in Allah from the devil`s evil suggestions that aim to distort the religion. Thus, once an organ is completely pure, don`t question its purity since having whispers doesn`t mean that the purity is invalid as it has already been established.

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.

How to pay Zakah (obligatory charity) due on articles of merchandise?

Articles of merchandise are estimated by their whole sale market price at the end of each lunar year, and (2.5%) of their value is paid as Zakah whether it (value) went up, or down compared to actual purchasing price, and whether the increase (profit) was in the article itself such as an increase in the animal`s weight, or in the prices themselves. And Allah Knows Best.

Is it permissible for the man to go out wearing shorts?

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

It is permissible so long as his Awrah (private part), which is between his navel and knee, is covered. However, the regular wear traditions and modesty are to be observed. And Allah Knows Best