You probably don't have two perfectly flat surfaces. So you are only making pure contact in a couple small areas. I would have re-routed the neck pocket, shaving off less than a millimeter, and then either hand flattened or belt-sanded the neck's heel. That can still be done now, but there're so many holes it's a bit late in the game to play armchair quarterback.
Some guys have put baby powder in there to alleviate the "lacquer against lacquer" creaks. That's okay I guess. Try countersinking all the holes slightly, both on the body and the neck.
Also it's entirely possible that some of your screws are threading the body. That's fine, and in theory it's advantageous. It actually helps to prevent neck movement. But if the neck isn't dead flat against the body, you can tighten the screws all you want and you're really tightening the neck plate into the body, but maintaining a slight gap between the neck and body. If this is the case, I would take out all the screws, ream out the four corner holes so the screws float freely in the body holes, but are still tight. Then install them, tightening the front two first, then the back two. Then reinstall your "overkill" screws, allowing them to thread the body as well as the neck.