I guess sometimes it's unavoidable, but I'm generally not a big fan of the mix and match itineraries you can ened up with through the online travel sites, for reasons which are illustrated by the OP. Unless the savings are significant, or the schedule much more convenient, I would much rather be ticketed on one airline so there is no confusion about who is responsible for any issues (I don't even really like codeshares, but that's probably taking it a bit too far).

As far as the OP's question goes - I don't think you really did anything wrong under the circumstances. You got about the best outcome that could be expected by following up with everyone involved until you found someone who was willing and able to help.