If I understand your question correctly, your problem is not being able to use pathfinder on a complex group of objects at once.
A simple solution is to convert the group to a compound path. With the group selected go to Object → Compound Path → Make or just hit CMD+8 (Mac) or Ctrl+8 (Windows)
Then you can duplicate the compound path and use pathfinder as you would normally.
Or Use a Clipping Mask
Another option, without using pathfinder, is to create a compound path as I described, then use that compound path as a clipping mask for the coloured bars. That way you can edit the shape and the colours without having to go through the whole destructive pathfinder process again every time you want to make a change.