Does an internal examination require ghusl?
Ghusl isn't required for making internal examination; however, it invalidates one's fasting. And Allah Knows Best.
Is it permissible for me to make up for my late father`s missed fasts? and should I make an intention to this end by saying: "I intend to make up for my late father`s missed fasts?
It is permissible to fast on behalf of the deceased father in order to make up for his missed fasts, and you should make the intention for offering fast from night time, but uttering the intention isn`t a condition. And Allah Knows Best.
What is the ruling on reciting verses of the Holy Quran on water, then drinking it?
It is permissible to recite Quran on water, then drink it as a kind of treatment since the Quran heals. Allah, The Almighty, Says (What means): "We send down (stage by stage) in the Qur’an that which is a healing and a mercy to those who believe: to the unjust it causes nothing but loss after loss." [Al-Isra`/82].
What is the best manner in distributing the meat of the Aqeeqah?
It is better to divide all of it as cooked meat amongst the poor and the needy. Dividing it into three portions is a Sunnah, but it is permissible to keep all of it provided that a portion, even a small one, is given to the poor and needy (one kilo for example).