How do I separate Materials in the compositor?

Witness this Blender Internal oddity.


I’d like to be able to affect the cloud layer/object with compositing effects. However, the cloud renderlayer has part of the orange sphere’s image coming through (where it overlaps in transparency) and part of the green sphere’s specularity at the back coming through.

Can anyone help me find a way to separate these influences out of the cloud renderlayer?

Cheers. Blend file attached.

https://dl.dropboxusercontent.com/u/13900881/transparencyLayersTest.blend

You’re getting way ahead of yourself. The first thing you need to do before asking questions like this one is to go and take some tutorials on Blender’s materials system. Once you understand how these materials and settings interact with one another then you will realize how ridiculous this question you have asked really is.