What is the best charity to offer on behalf of the deceased? Is it giving food, reciting Quran, giving money or supplicating? What is the best charity to offer on behalf of dead father and dead husband? What is the best continuous charity to offer on behalf of the deceased?

Praise be to Allah the Lord of the Worlds. The deceased benefits from every righteous deed offered on his/her behalf, be that continuous charity, reciting Quran or a pious son praying for him/her. However, the best righteous deed is performing Haj and Omrah on their behalf especially if he/she hadn`t performed that ritual for it remains a debt on them. The evidence on this is that Ibn 'Abbas (Allah be pleased with them) reported: A man came to the Messenger of Allah (PBUH) and said: "Messenger of Allah, my mother has died (in a state) that she had to observe fasts of a month (of Ramadan). Should I complete (them) on her behalf? Thereupon he (the Holy Prophet) said: Would you not pay the debt if your mother had died (without paying it)? He said: Yes. He (the Holy Prophet) said: The debt of Allah deserves more that it should be paid."{Related by Muslim}. And Allah the Almighty knows best.

Is it permissible for a person who has to make up for missed fasts to fast six days of Shawwal (the month directly after Ramadan) before making up for the missed fasts?

Yes, it is permissible for him/her to do so, but it is better that they make up for missed fasts first. And Allah Knows Best.

What is the ruling on working for orphans' institution?

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.