I believe this hinges on the basic nature of stacking:
one specific unit cannot stack with itself just because it is valid to be counted by multiple abilities.
Stacking is by definition combining the effect of different units, not re-counting the same one.
So a given class level will only count towards animal companion level once.
Animal Ally is a seperate 'unit' from actual class levels.
AA is based on character level, which basically means it is class agnostic. But if the component levels of total character level are already being counted (whether from other total character level-based abilities, or class-based abilities), then you shouldn't double count them because that is not 'stacking' but is now 'double counting' which AA and other Companion abilities don't allow, they only allow 'stacking'.
No. Animal Ally ceases to function, as you no longer qualify for it.
