Is it permissible for someone to make a supplication to Allah to marry an already married, or an engaged woman?

No, it isn`t, and the person who does so is sinful before Allah, The Almighty.

For passing time, my friends and I have called a famous diviner. She told me that somebody had cast a spill on me not to get married for the rest of my life. I didn`t believe her, but I can`t forget her words. How can I protect myself from such thing?

Praise be to Allah the Lord of the Worlds.

Dealing with diviners is forbidden and what you are suffering from is due to your having consulted that diviner. Have trust in Allah and ask Him for forgiveness, but rest assured that whatever Allah has decreed will take place. And Allah The Almighty Knows Best.

What is the ruling when the duration of the monthly period varies, and sporadically increases?

If the period didn`t exceed (15) days from the first seeing of blood discharges until its end including the times of temporary cessation, then it is menses. But, if the period exceeded (15) days, then the woman experiencing this is Mostahadah (bleeding outside the time of monthly period), and should abide by her regular period, and consult one of the scholars.

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.