Is it permissible for a Muslim physician to specialize in gynecology obstetrics, and what is the ruling on working as such?

Some fields of knowledge are an individual duty while others are a collective one, and specializing in gynecology obstetrics is a collective duty. However, if there were female physicians to treat women, then there is no need for a male gynecology obstetrics specialist to look at women`s Awrahs (private parts) except in necessary situations since the jurisprudential maxim says:” Necessity must only be assessed and answered proportionately.” And Allah Knows Best.

Is it permissible for a woman to offer the obligatory prayer after Adhaan (call for prayer), and before Iqamah (The announcement that the prayer is about to begin) in the mosque?

 

Yes, it is permissible for a woman to offer the obligatory prayer immediately after the Adhan and before the Iqamah in the mosque. And Allah Knows Best.

The supplication: "O Allah, we do not ask You to avert the decree, but we ask You for kindness in it." Is this Supplication Halal or Haram?

We are obliged to supplicate Allah, so when supplicating we comply with Allah's Ordainments, and making supplications that are reported in the authentic texts is better. 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