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 Zakah (obligatory charity) due on the money saved for marriage?
Zakah is due on the money saved for marriage if it reached the Nissab (minimum amount liable for Zakah), and a whole lunar year had lapsed over possessing it.
Is it permissible to single out Fridays, Saturdays, and Sundays to make up for missed fasting without fasting a day before ,or after each ?
Yes, it is permissible to make up for missed fasting during the aforesaid days, and it is also valid to offer non-obligatory and vowed fasting as well. However, fasting a day before or after each isn`t obligatory. And Allah Knows Best.
Is it incumbent on a father to cover the marriage costs of his son if the latter couldn`t afford them?
The son should seek the help of his relatives in order to convince his father to do the aforesaid, and the father should make sure that his son doesn`t commit fornication through helping him to get married, and Allah will reward him for doing so.