What is the ruling on agreeing with a tenant to construct only two floors of the agreed-upon building, on the condition that he pays the cost of the third floor in cash, given that the current construction does not comply with engineering or municipal requirements?

Since the individual did not adhere to the agreed-upon construction, you have the right to annul the contract. And because removing the structure would harm its owner, the possible method is to consider the first contract null and void, then conclude a new agreement that benefits the endowment and does not harm the property owner, by setting the rent for the endowment land in its current state at the prevailing market rate. It is necessary to refer to the Sharia court or to scholars knowledgeable about such contracts pertaining to endowments.