Here is my solution. I'm still hoping there is a way to create physics joints with the scene editor but I haven't found it so...
Step 1) Add all the child nodes to the scene, ensuring that objects are grouped by parent.

Step 2) Define a swift class for your complex node.
class MyNode : SKSpriteNode {
func spawn(parentNode: SKNode, position: CGPoint) {
parentNode.addChild(self) // before physics joints
let arm = self.childNode(withName:"arm")
// note if you didn't add physics bodies in scene file
// do that first
let shoulders = SKPhysicsJointPin.joint(withBodyA:self.physicsBody!, bodyB: arm.physicsBody!, anchor: CGPoint(x:position.x,y:position.y-1))
scene!.physicsWorld.add(shoulders)
// feature of pulling a child from a scene, it's always paused by default.
self.isPaused = false
}
}
Set the class for your body node in your scene.

Step 3) Transfer your node to your game scene at init time.
let tmpScene = SKScene.init(fileNamed: "MyNode.sks")
var myNode = tmpScene.childNamed(withName:"myNode") as! MyNode
myNode.removeFromParent()
myNode.spawn(world, position) // or your own parent and position as needed for your scene