Ok. So when you say you had him sit, you mean just in his container? That would acclimate water temperature, but would not acclimate varying types of water PH levels and such.
Usually the best way to acclimate is leave in a container, like you did, but occasionally add a very small amount of water from the tank. Let it sit 10 minutes, then add a little more.....do this until most of the water is changed out and he's in the fresh tank water. That way it's not a shock to his system.
But it's kinda late for that now, and I'm sure it's nothing you did. I'm not sure what else to suggest except just hope he will make it and be alright. :(