Is it permissible to offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?

It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.

Is the `Iddah (waiting period) of the divorced effective from the time the divorce took place, or from the time of registering it at the court?

It is considered effective from the very moment her divorce took place, but not from the time of registering it at the court. And Allah Knows Best.

Is it permissible for a wife to boycott (not to attend to his different needs) her husband?

It isn`t permissible for the woman to boycott her husband unless he is the reason behind that, and it is recommended that both spouses seek the advice of righteous people to make reconciliation.

Should I pick up the newspapers thrown at the street because they definitely contain sacred names?

All perfect praise be to Allah the Lord of the Worlds. May His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.

The Messenger of Allah (PBUH) says: "Be mindful of Allah and He will protect you." Part of this is protecting whatever contains the name of Allah. Therefore, if you see a paper containing Allah's name thrown in the street, then you should grab it and similar papers, then burn them in a clean place. Doing so is permissible because Othman (May Allah be pleased with him) has burnt copies of the Quran which didn`t match the main Mus-haf. However, you aren`t required to collect every paper in the street. And Allah The Almighty Knows Best.