Swift / SpriteKit - Can't break strong reference cycle

I completed a spritekit game without having knowledge of strong reference cycles. I'm not having any crashes or obvious problems, but using instruments I can see my objects being retained between each level (SKScene should be dealloced between levels).

Here are the general pieces of my game:

GameConfig static struct

I have a globally accessible static struct that references my ViewController. I access the viewController using this struct from all over the app. I assign GameConfig.viewController = self inside of the viewController's viewDidLoad

GameViewController

In here I reference my SKScene, and SKView as such

var skView: MyView!
weak var scene: SKScene!

BaseScene

This is my base SKScene class. This is the only property of this class that gets a reference to the class itself

let indicators: Indicators = Indicators()

KillScene subclass of BaseScene

In my BaseScene subclass, I have many custom subclasses contained in arrays. These custom subclasses do reference the scene, but the scene is not referencing them directly. It only has reference to their container array. Example:

var radarBlips: [RadarBlip] = []

I do have one property that has a strong reference cycle with KillScene

var ship: KillShip = KillShip()

In both my Indicators and KillShip classes, I have referenced my scene using the weak keyword.

In fact I have found every instance where I reference the scene, and put weak in front of it.

I tried to make a stripped down game, and create a strong reference cycle between a sprite and a scene, and then break it. I was successful in doing so. But I can't seem to debug my own game.

Any detailed suggestions would be helpful. I know there's trickiness with passing closures around. Maybe that has something to do with it? Any advice on what I could look for would be great. I've put weak in more places than I probably need to.

I can not get the scene to deinit