Your experience pretty much matches my own, especially the 5am Chicago drop-off (could they have put better signs directing you there?). One thing they didn't tell me until I got there is that the pet needs to be able to stand up completely while in the kennel, and there are different tolerances for international vs domestic flight. So while the carrier my cat was in met the US standard, it was too small by international guidelines. Fortunately someone had donated a kennel that was big enough, so that was the only hiccup to the process.
Thanks, I forgot that part. At ORD my dogs ears did touch the top of the kennel. I explained that I had just driven her 12 hours to get to ORD, so I was hoping she would be fine (she was able to sit with no problems), she has big ears (she does, I almost named her "Radar"). When the manager came out, the check in rep explained what I had told her, and that the next largest kennel wouldn't fit on the airplane. He looked at her, grumbled a bit, and said "Ok."
Yes, the signs to get there, half asleep, in the dark, left a lot to be desired (I drove past it the first time).