Question: How does Don Self know that Miriam should work at Gate when nobody knew about the location of Scylla? Or Whistler wanting to work there?
Answer: Because Miriam was an agent.
But that still doesn't make sense because nobody knew where Scylla was.
He knew that GATE was mentioned in the bird book. He worked with Whistler and had probably discussed GATE with him, so it was clear enough that it was a big part of the plan to get Scylla. Sending an agent to work there in any position would've been a big help for intel, as she could assess the environment and perhaps uncover what Whistler's plan was. He didn't anticipate T-bag's hijacking of the plan, hence why he sent Miriam and not a more combat-trained agent. She was only there for information.
Question: I don't understand why Pullo is so angry with Vorenus and thinks he needs to apologise. Having fought in Caesar's army for as long as Pullo has he would be very well aware of the repercussions for what he did, why would he blame Vorenus for abiding the law and doing what is required of him as a centurion?
Answer: Its Pullo's nature to resent people of higher standing than him. His jealousy of Vorenus in later episodes, which in part leads to their falling out, is proof of that. From Pullo's point of view, Vorenus just got better breaks to get where he is in the army and so, isn't really his superior. That, plus his natural arrogance is explantion enough for his behaviour in spite of the fact that he broke the rules and was being fairly punished.
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.