How does animal attunement work in official play?
Pretty much as specified in the book.
Are we allowed to do it?
Yes.
How do we get the animals (find or purchase)?
For Missions, Animals can only be purchased using the availability listed in the charts in the Howling Shadows section of the FAQ. A dash indicates always available with no license requirement.
How do we get warform versions of animals (and what are the costs)?
Currently, the determination for purchasing the base variant of a Warform have not been considered for Missions. This looks like an oversight and might be updated in time for Origins. Until then, Warforms are not available.
Are we limited to the selections in the "Hollowing Shadows" portion of the SRM Combined FAQ?
That's what it says.
Does the FAQ's animal limits for lifestyles apply to attuned animals (effectively limiting the number despite initiation ranks)?
Yes. The idea is that if you cannot adequately provide to the needs of the animal without that level of lifestyle. Obviously this isn't completely true to life (a squatter in Chicago could surely have an entire pack of dogs!) but is a balancing function.
How EXACTLY do we use the Animal Handling skill when roll playing out commands (i.e. Hit ratings for complexity of actions, like "move or attack = 1 hit" vs "track the scent = 2 hits" vs "sneak around back and wait for my signal = 4 hits")?
Howling Shadows very specifically lists training and commanding animals on pages 183-185. Note that training is a downtime action, since it requires at least a week be set aside for the training.