Is living above one's parents considered an act of disobedience (ʿuqūq)? What should I do to please everyone after my wife's behavior towards my parents? And does parental satisfaction negate previous shortcomings of children towards them?

There is no harm in residing on a floor above the parents' floor, as long as they are content with it. Indeed, the lower floor might even be more comfortable for them. The feeling of falling short towards parents is natural due to the enormity of their rights, and one should strive to please them as much as possible. Their satisfaction with their children atones for any potential shortcomings. As for the wife's apartment key, she has the right to keep it or leave it with whomever she wishes. It is best to try and appease the husband's mother and assure her that the matter is not about mistrust. It is preferable for the wife to placate the husband's mother by leaving the key with her if no harm results from it, for honoring the husband's family is a way of honoring the husband himself.