Is it permissible to swear by (Allah "The Living")?
Yes, it is permissible because "The Living" is one of Allah`s Attributes.
How should I be kind to my atheist father?
Allah, The Exalted, has decreed and ordained his slaves to be kind with parents, even if they are polytheists, by honoring and obeying them in all that isn`t sinful, so that they might love Islam and embrace it as a result.
Is Making up Missed Obligatory Prayers an Obligation?
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 of his family and companions.
Missed obligatory prayer/prayers is a debt upon Muslim and making it up is an obligation, since the Prophet (PBUH) said: "pay the debt due to God, for it is the one which most deserves to be paid." [Agreed upon]. And Allah Knows Best.
What is the ruling on working for orphans' institution?
Praise be to Allah the Lord of the Worlds. May His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
There is no sin in working for orphans` institution. And Allah The Almighty Knows Best.