What is the ruling on istibra' and how is it performed?

Istibra' (cleansing from urine) is recommended. It is for a person to ensure that nothing remains of urine in its passage before performing istinja'. Its method is: to clear the throat (or cough slightly), shake the penis (meaning to pass fingers along it to expel any remaining urine if needed), and walk a few steps to the extent that one thinks nothing of urine remains if walking is needed. Each person knows his own nature best. The preferred opinion is that this differs among people. The objective is for one to think that nothing remains in the urinary passage that he fears will exit later. And Allah the Almighty 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. 

What should a person, who doubts the validity of his Wudu, or over performs it, do?

One who doubts the validity of his/her Wudu while performing it should redo it until he/she is certain of having attained purity. But, if doubt was after having performed Wudu, then he/she should not pay attention to that as doubt after the end of an act of worship does not count. This is of course in case doubt was within the reasonable limits since once it goes beyond that, it becomes a whispering of the Shaytaan (devil) which he/she should ignore as the Wudu is valid.

I am a woman, and my natural menstrual cycle lasts six days. In the evening, I perform the testimony (Tashahhud) for myself, and then I engage in sexual intercourse with my husband. After intercourse, I experience bleeding, either immediately or the next day. Is my intercourse with my husband during this time forbidden?