What is the ruling on living in a house built by a father for two of his sons, and not for all of them? And does paying rent to the father for living there solve the problem of fairness among the children, especially if it will be deducted from the children’s share of the inheritance?

The father's fear of wronging his daughters is valid, and he must be just among his children, male and female, in gifts and benefits, as narrated from the Prophet, peace and blessings be upon him: "Then do not make me a witness, for I do not bear witness to injustice." It is permissible to prefer some children in giving for a legitimate reason, such as need, illness, engagement in knowledge, or if the other child is an unrighteous person or an innovator.

Therefore, there is no blame on your father for lending you housing without rent due to your need and your sisters' independence from it, as this is a preference with a valid justification. As for calculating the rent from the inheritance, it has no consideration, for inheritance is not owned until after the death of the inheritor.