I assume wild shape armor would not apply to the swarm ac's, but just confirming.
The real question is, since i have complete control of the swarms that my body has become, could i be in an enemies square, and an allies, and CHOOSE not to harm the ally?
The spell states that your armor gets left behind, and the spell isn't "wildshaping". So I agree that the ac bonus from Wild armor wouldn't apply after you cast the spell.
As for the other question, the way the attack is worded, I think you can either attack everyone or attack no one. Now, if you have broken yourself into multiple swarms and Swarm A is in an enemies square and Swarm B is in an ally's square, Swarm A should be able to attack independently from swarm B.
Swarm Attack: creatures with the swarm subtype don’t make standard melee attacks. Instead, they deal automatic damage to any creature whose space they occupy at the end of their move, with no attack roll needed.