Initially I started with this setup:
Now with top shelf added:
When I attached the top support sheet, removing the receiver from the top of the APM itself, and moving it to the top shelf, my vibrations increased quite a bit.
They went from this:
I'm thinking that with the receiver on a non-vibration shielded part of the quad now, the vibrations are being carried through the wires to the APM.
I'm going to try a different type of O-ring first, to see if that will have a positive effect on the vibrations. Switching from the red silicone o-ring size 017 to a smaller nitrile o-ring size 015.
Also, in the intial setup I had the APM attached to the base via a direct velcro strap. I've now added some silicon gel underneath the strap so the APM is only touching its supports through vibration dampening gel.
Now awaiting a battery charge to see how the new setup performs....