Is permissible to buy/sell with non-Muslim?

Yes buying/selling for a Muslim with non-Muslim is permissible as regards what is lawful.

Is the marriage, which lacks a valid legal contract, a guardian, and a court registration, valid?

It is incumbent that a valid marriage contract be concluded in the presence of a guardian and two trustful witnesses, and it should be registered in the court to protect the rights of the wife. Actually, a valid marriage contract is what differentiates between sound marriage and fornication.

Is permissible to include a will requesting that a Holy Qur'an buried along with me?

It is not permissible to include a will requesting that a Quran be buried with the deceased in their grave. This is because the body of the deceased typically decomposes and may release impure substances, and it is not allowed to expose the Quran to impurity. Intentionally desecrating the Quran is an act of disbelief. Instead, read the Quran during your lifetime, as it will benefit you after death. And Allah Knows Best.

I work for a company whose manager refuses to allow employees to leave during work hours. Do I incur sin if I secretly went out to join the congregation at the Masjid? Is doing so considered a breach of trust?

Praise be to the Lord of the Worlds.

We recommend that you pray at work to encourage your colleagues to follow suit, because whoever guides to good has the like of the reward of the person who actually does it. And Allah The Almighty Knows Best.