Whistling and pooping are excellent signs. Whistling means he's not feeling too bad and pooping means his digestive system is still working.
It looks like there's a piece of skin or something sticking out from the wound near his nostril. This isn't a problem in itself if the area that it came from has formed a scab. Can you tell what's happening with the wound on the side of the beak? That's the one that worries me the most, it looks like it could be deep.
Do you think there's any chance that an animal could have tried to get the birds through the wire and he got clawed? The biggest risk from that would be bacterial infection.
I don't know if this will help you feel any better, but here's cknauf's thread about a beak injury that Denali had. It's not quite the same as Tommy's problem, but it was expected to heal without any problems:
viewtopic.php?f=15&t=1659