Why were both the families and the guards told that the other had died?
The families were told that the guards had died by the government. The guards were told the same by whatever mysterious force took them away. We may assume they are not one and the same.
Why are even the guards turning into criminals?
Some form of compulsion seems to be at work. The Returned seems to have been implanted with some basic directives. For Jack Sylvane, it was 'recover the key'. For Guy Hastings, 'find Tommy Madsen'.
What is the point of building an Alcatraz replica? Why bring all these dangerous criminals all back into one place?
Where else will the government put them? They can't put them in normal prisons.
I'm sure we've come a long, long way in 50 years in terms of super maximum security prison design. Yet the replacement jail is a structural replica of C block. The 63s even go into the same cells as they had back then. It's more than just a tough jail. It's the same freaking thing, except with brighter walls.
I don't think they're going into the same cells. They have Jack and Cobb next to each other and I'm pretty sure they weren't in old Alcatraz. I think they're just putting people into cells depending on when they get caught for the sake of convenience. And it's not exactly the same as old Alcatraz. For one thing, they have cameras watching everything and I'm sure there's some sort of advanced lock for getting in and out.
Who are the people in the Room, and why does Hauser keep them separate from Madsen and Soto?
This probably has to do with Hauser's trust issues. He doesn't seem to want Soto or Rebecca to know any more than what he tells them.
What were Rebecca and her partner chasing Tommy Madsen for?
We don't know yet.
Why did Tommy Madsen attack Ray at the prison?
Actually Tommy gives a partial explanation for this. "You shouldn't have come here!"
He wanted to communicate this message without anyone else hearing and getting Ray in trouble so he made it look like a random attack and quietly suffered the consequences.
Is there a meaning or back story behind Cobb's "47 slats in the picket fence" chant?
My personal theory is that he is referring to the home of the mother who abandoned him and the sister she didn't. That whole situation clearly had an effect on him, given his later killings, and it wouldn't be too strange to imagine him staring at that house through his scope and memorizing every agonizing detail of the life he was denied.
Why is Ray surprised to see that Guy hasn't aged, even though he is already aware that Tommy hasn't either? Why has Ray kept this quiet? And obviously he now knows that Rebecca knows the secret too.
For the first question, perhaps it was an act to keep Tommy's presence a secret, by being surprised he implies he hasn't seen another unaged person such as Tommy.
Where did Sweeney get a captive-bolt pistol from? Especially since they are no longer used. Also, how is he killing people with it, since they are designed to only cause unconsciousness?
There are bolt pistols that can kill, and since they are still used in some places, it could have been easy enough to steal one from a vet or slaughterhouse.
Who planted the return ferry ticket and locker key in Sylvane's jacket?
Part of the mystery.
Why weren't the really awful serial killers like Johnny McKee or Kit Nelson sentenced to die? They were imprisoned in the 50s or very early 60s and child killers or mass poisoners would have likely gotten the death penalty.