You've got a winner!!
i dont have any easy solutions for you but maybe a few things to think about....
conditioning constant outside air can be a huge heat load and can cause humidity issues. an ERV (energy recovery units) may help with this.
carbon filters are expensive but may help with the smell.
you may also want to see if any of the returns for the 2 ton unit are in the dog kennel area.
and obviously fix the conditioned air being discharged out the roof