Are the funds generated from my father's building permissible or impermissible, taking into account that the land on which it was built was acquired by "وضع يد" (squatting/adverse possession) and my father bought it from those who had acquired it in the same manner, and that the construction was done without a government license and with more floors than permits allow, and my father did not commit to building a car garage but instead built commercial shops?

It is permissible to take possession of land that is not owned by anyone and has not been taken possession of by the state, to revive it, and to benefit from it. Otherwise, it is not permissible. If the possessor is a usurper, then buying it, benefiting from it, building on it, selling its apartments, and renting them out is forbidden. However, if the possession is permissible, or the state approves it, there is no harm in benefiting from it. Building without a permit does not make the price of selling the apartments or their rent unlawful. Similarly, not constructing a garage does not make the price of the shops or their rent unlawful, even if the father sins by violating the laws.