Try this two lines (MEL), for me works even if multiple empty groups are parented together as in the example image above. source cleanUpScene.mel; deleteEmptyGroups();
You won't be able to bake if you are linking. The baking tools have never supported a parent/child relationship. You will want to use constraints, then bake.
Correct me if I'm wrong, but can't after effects cs6 access the layers from a PSD directly? Or doesn't that work with positioning and parenting as you need it?
The ceiling looks like my parents basement , it has ceiling panels, Atm the lighting needs work, The textures need more Variety everything is a pattern.