Is the wife's father obligated to pay the remaining amount for the car, given that he guaranteed the buyer and the latter did not pay the full amount, and does the wife's father bear the penalty for the shortfall in the amount after deducting what he paid in penalties?

If your wife's father guaranteed the car's price to the buyer, then he must pay it to you, and he can then seek reimbursement from the buyer for what he paid. However, if he was merely an agent for selling the car and bringing its price, he is not liable unless there was an act of transgression or negligence on his part. So, if he was negligent in collecting the price, then he is liable. As for the fines your wife's father paid, and you both agreed that these would be deducted from the car's price, there is no harm in that.