Good you got it working. I've spent a long time messing with it since my post. What's been working really well for me is creating a subscene that the CUA and effectors are tied to. My problem with parenting undoing itself was solved by using the subscene atom as the parent.Just messing around more and think I found where I was going wrong. I was renaming the ik atoms to make it easier to identify. It was breaking them. Now it works!
What surprised me is it even worked if I loaded this subscene in a different scene. Even multiple instances of the same one.