KeyCue reveals shortcut key combinations for nearly all apps and macOS itself. I say “nearly all” because a few apps use non-standard menus and KeyCue doesn’t always find shortcuts for them. It has a “learning mode” that is supposed to overcome that but I’ve had mixed results with it.
There’s also CheatSheet, but I don’t have any experience with that.
Sorry, I can’t help with the preferences problem, although I, too, experience it. Apple keeps moving stuff around, which doesn’t help.