What is the ruling on someone who prays Fajr late, after sunrise, knowing that they wake up on time but return to sleep and do not perform it within its time?
It is obligatory to perform the prayer within its prescribed time. If someone wakes up and knows how to act, they must perform it before the time ends. If they delay it, they are sinful and must make it up. And Allah Knows Best.
Should a pregnant woman who broke fast because of pregnancy make it up, and is a ransom due on her?
The pregnant and the suckling, if they fear for their health, may break their fast and make up for it, and no ransom is due on them. However, if they broke fast in fear for the fetus and the baby, then they are obliged to make up for it, and pay the ransom which is feeding a needy person for each of the missed fasting days. And Allah Knows Best.
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.