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I was probably a bit unclear - you should be able to combine all 3 parts into a single mold  for $3k, so 1000 units would run about 5k total.  Even if you wanted to do separate molds (for contrasting colors or just to not have to clip apart the pieces), you still only need 2 molds since the outer shells could be identical if they aren't already.  So maybe $5k for tooling if you go that route. 
Certainly, get some solid quotes and run the numbers, but IMO there is a lot of potential upside here, and this is the kind of project that the maker community really gets behind.
What software did you design in?  Most 3D CAD packages have mold design tools.