The answer to your question about things getting worse before they get better is YES! Things do get worse before they get better, it's the axiom of healing...oddly enough. His body and tissues have suffered trauma, his body and immune system are doing what they can (swelling to create a cushion to protect undamaged tissue as well as to create a sort of "brace" for damaged areas, etc). All you can do is give supportive care like epsom salt soaks. electrolytes and meds (btw the suggestion to get your hands on Penicillin through fish meds was brilliant!).
Aubrey, if he's fighting you it could be the energy with which you are approaching him. You're stressed out. Every time you look at him you're tense, upset, worried...he FEELS that. So why would he be cooperative with someone who's coming to him with all this anxious, negative energy? Calm yourself, he's been through hell...which is why he looks like he did -- accept that he looks roughed up. Literally come from the center of your chest with how much you love him and are there to help him. Right now he needs YOU to be the calm and safety he's looking for. He saved the girls, now you're there to save him...not the other way around. Know what I mean?
We almost put too much on our animals when we're stressed...as if our happiness depends on their healing. WHOA! Too much for an injured animal to carry. Right now it would be nice if he got his appetite back. (And of course our happiness teeters on their well-being, we can't help it) But he needs you, more than you need him at the moment, so get your emotions in a healthier place and you will get much more cooperation from him.
You wouldn't want your doctor approaching you with a, "Geez, I hope she makes it?!" attitude, neither does Petey.
Breathe...