Sounds like you're getting it sorted out. Here's part of the problem. We're driving cars with over 100k miles on them, sure there's parts that wear, and when they're replaced, it puts strain on the next weak link. So the love/hate relationship continues, it's a good thing your car has an owner like you.
You might try this...
With the car parked, bounce on the rear bumper up and down to try to simulate the knocking sound. (leave the e-brake off, it will make noise if you don't) If you still can't get the car to replicate the sound, go around to the rear wheel well and reach down and pick up on the inside of the fender and see if the sound is when the suspension is retracting. If you can replicate the sound while doing this, you'll need another body to help pinpoint where the noise is located.
What comes to mind are rear shocks, mounts and even broken springs. Good luck with your search.
JR