Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
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 Zakah (obligatory charity) due on the items used in the trading process such as: cars , shops etc..?
No Zakah is due on equipments used in the trading process such as cars and the like.
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.