Is Zakah (obligatory charity) due on the Zakah money received by a poor person, and reached a Nissab (minimum amount liable for Zakah), and a whole lunar year had lapsed over having it in his possession?

Yes, the poor who possessed a Nissab for a whole lunar year is obliged to pay the Zakah due on that money even if it was given to him as a Zakah money in the first place. And Allah Knows Best.

When Iddah is Initiated for Deceased's Wife?

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.

Iddah is observed on the same date at which her husband passed away for four months, but as for the pregnant, it is observed at the date she gives birth. And Allah Knows Best. 

Is Zakah (obligatory charity) due on articles of merchandise even if they were stacked in the merchant`s stores for years?

Yes, Zakah is due on goods even if they were stacked in merchant`s stores for years, in this manner Islam struggle against monopoly.

Is it permissible for me to make up for my late father`s missed fasts? and should I make an intention to this end by saying: "I intend to make up for my late father`s missed fasts?

It is permissible to fast on behalf of the deceased father in order to make up for his missed fasts, and you should make the intention for offering fast from night time, but uttering the intention isn`t a condition. And Allah Knows Best.