Who should pay the Zakah (obligatory charity) from the orphan`s money?
His/her guardian, and if the latter fails to do so, then the orphan himself/herself is obliged to pay the Zakah once he/she reaches puberty, and is capable of handling his/her own affairs. And Allah Knows Best.
Who is the one required to slaughter the 'aqīqah?
All praise is due to Allah, and may peace and blessings be upon our Master, the Messenger of Allah.
It is Sunnah for the 'aqīqah to be slaughtered by the guardian of the newborn — the one upon whom the child's financial maintenance is obligatory — provided he is financially capable of doing so. 'Alī ibn Abī Ṭālib, may Allah be pleased with him, reported: "The Messenger of Allah ﷺ performed the 'aqīqah for al-Ḥasan with one sheep." — Narrated by al-Tirmidhī. And Allah Almighty knows best.
Is it permissible to give multiple mudds (portions) of fidyah to a single person?
Yes, it is permissible to give multiple mudd of fidyah to a single person, because each day of fasting is considered an independent act of worship.
Is the father a Mahram (Non-marriageable) to his son`s mother-in-law?
The father is a non-Mahram (Marriageable) to his son`s mother-in-law, so it is impermissible for them to look at each other, or to have a seclusion (Khalwah).