I am a disabled woman who has vaginal discharges and can`t control her urine. Therefore, I combine prayers. Is that permissible?

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 his family and companions.

According to the Hanbali doctrine, it is permissible for the sick to combine prayers. In your case (Asker), it is better that you delay the noon prayer until a few minutes before the afternoon prayer in order to minimize the time span between the two and perform each alone. In addition, you can do the same with sunset and evening prayers. Finally, we ask Allah to bless you with recovery. And Allah Knows Best.

Should missed Sunnah prayer be made up?

Making up missed voluntary acts of worship is from Sunnah.

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 a young man and a young woman to enter into a covenant as a married couple without having a true seclusion (Khalwah) until their marriage contract is officially concluded?

The relation which isn`t based on a marriage contract is forbidden, and entering into a covenant as a married couple is unaccounted for and is from the evil suggestions of the devil.