I see the last link mentions using an intrinsic map. I suspect you've not done this. Any time you have bad performance, it's worth your while to use a tool like YourKit to measure what specifically is so slow. It's likely this would point at org.eclipse.emf.ecore.resource.impl.ResourceImpl.getEObjectByID(String) as a bottleneck and then you'd look at the code and quickly see how the intrinsic map would improve things:

  protected EObject getEObjectByID(String id)
  {
    Map<String, EObject> map = getIntrinsicIDToEObjectMap();
    if (map != null)
    {
      EObject eObject = map.get(id);
      if (eObject != null)
      {
        return eObject;
      }
    }