Ok, so I got bored with the effort of moving my hand to the mouse to click a team member when I wanted to swap in the middle of a battle. It was a pain being able to do everything with the number keys (1-5) and there wasn't a key to pick a pet. It turns out the following can be used:
PetTrackerBattleSlot4 (top pet)
PetTrackerBattleSlot5 (middle pet)
PetTrackerBattleSlot6 (bottom pet)
So, if you make a macro for each one with the click command and bind it to a key (I use alt+1, alt+2, alt+3) you can do the whole fight with just the keyboard. For example, to pick the top pet the macro should be:
I hope that helps somebody.