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: In this episode they are digging the hole to get through to 'Scylla', when digging the hole the concrete bar drops or something. Brad goes in to the pipe help but he can't get out in order to get them to Scylla, so therefore he is left in there to die. That tunnel though is the source of the water to L.A. So there would be a dead body in the water and everyone would be drinking water where a dead guy was, am I right? Or did I miss out on something?
Answer: They got Brad's body out.
Answer: Yes you are right, the entire city of LA was drinking water contaminated by a dead body.
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.