Is it legal for a father (custodial parent) to list his son's name on his school information cards with his (father's) last name, even if his son's name is the mother's maiden name on his birth certificate?

Yes it is legal. Anyone can use any name they want as long as there is no intent to defraud. Its actually quite common for the custodial parent to use a last name different from their legal name when registering a child for school. The school will still require that records indicate the legal name, but will allow the child to be referred to by a different name for anything but official records.