Hi John, sorry for the delay:
I'll try to answer your questions in order.
1. I'm not sure I'm understanding correctly what you want to do, but wouldn't adding the cube as child of the plane or vice-versa help? That way you'll be able to rotate a single pivot3d object and its children will rotate relative to the parent.
2. I think there's only one little thing missing from your code, you need to force recalculation of the numTriangles property, something like this:
surface.numTriangles = -1;
You can find a complete example here
3. Yes. Unfortunately, fixing that also makes event to arrive to the Stage3D even when you've clicked over a Flex button and we haven't found a way to stop that from happening. I put together a small, rather basic example you can download here
. Please note that it's a FlashBuilder 4.6 project and you have to provide your own Flare3D SWC.