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.

Is it permissible to offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?

It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.

Is it permissible for a woman who is in her confinement to fast upon seeing blood signs that are neither black, nor red ?

Brownish, reddish, and yellowish discharges are all considered confinement until there is no colored discharge which marks the end of confinement. Moreover, the aforesaid woman is prohibited from fasting until she attains ritual purity. And Allah Knows Best.

After I had prayed, I found a drop of menstrual blood and was unsure when that happened; what is the ruling on my prayer and fast?

All praise is due to Allah, peace and blessing be upon the Messenger of Allah.

Your prayer and fast are correct ,and you should not make up for them, and we ask Allah, The Almighty, to duely reward you for these acts of worship. Your menses start once you see blood because the situation remains as such unless there is certainty or predominant conjecture, as per the Fiqh maxim: "Certainty is not removed by doubt". And Allah Knows Best.