Cookie-style cutter trimming of all ungrouped objects?

[Patch97236]

I'm trying to ungroup all objects, then select them all, and in pathfinders select trim. My goal is to have only non-grouped objects without any overlaping objects, cookie cutter style trimming. I'm having a problem with the objects creating a shadow effect with opacity, since I want to retain the darkened color and make objects out of the shadow objects.

The problem is with objects similar to the selected object, the trimming produces two objects, when I only want one object with the darker green.

 

How can I get a cookie-cutting style triming where I only have single non-overlaping objects? Do I have to remove opacity from all objects first, then trim all obects, and then darken the object fill colors to have the same effect?

[Patch97236]

I've included the .eps file I'm working with.