Is it incumbent on a husband to pay the alimony of his wife if she had left him and stayed at her parent`s without his permission?

When a wife leaves her house, and stays at her parent`s without asking her husband, she is considered a Nashiz (wife who refuses to abide by her husband’s orders), and so she doesn`t deserve an alimony.

Is Zakah (obligatory charity) due on the items used in the trading process such as: cars , shops etc..?

No Zakah is due on equipments used in the trading process such as cars and the like.

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 it permissible to make up missed prayers at the times in which praying is disliked?

All perfect praise be to Allah,The Lord of The Worlds                                                                                                                                                                        It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.