I have seen quite a few large flocks of Canadian Geese migrating around Chicago lately. From what I have read they were "large birds." Other than geese, I'd guess they could have also have been cormorants, although I'm not sure if cormorants flock together when migrating. Are there other large birds that flock together and are currently migrating through the Chicago area now?
As far as engine damage, other than someone from UAL chiming in, we'd have to guess that one engine was pretty much destroyed, and the other one, which IIRC may have only ingested one bird, was in a repairable condition.
What scares me is that they could have just as easily lost both engines. And with a full load of fuel for the flight to San Paulo, things could have been pretty disastrous.