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.
What is the ruling on the ablution of one who touches his wife without a barrier?
In the Shafi'i school, a man's ablution is invalidated by touching his wife if their skins meet (in any place) without a barrier, whether the touch is intentional or accidental. An exception to this is touching hair, teeth, or nails; these do not invalidate ablution. And Allah the Almighty knows best.
Is the marriage contract considered valid if concluded at home by the marriage official (Ma`zon)?
Yes, it is valid as long as it is registered at the court.
How should I deal with the whispers of the devil with regard to ablution and purity?
Whispers in ablution are from the devil, and so you should take refuge in Allah from the devil`s evil suggestions that aim to distort the religion. Thus, once an organ is completely pure, don`t question its purity since having whispers doesn`t mean that the purity is invalid as it has already been established.