I think "Guardians" either refers to the responsibility of Amy and Dan to guard the ring from the Vepsers, or the responisibility of the Madrigals in general to do the same.
As for "Damien is Alive," I don't see how Damien Vesper could be alive in the 21st century, either. However, at the end of the second part of Vespers Rising, *spoilers hidden; highlight to see* it is implied the Damien died. It's possible that he actually survived the accident. It would explain several things. The code is one, but, personally, I was surprised to discover in Vespers Rising that Damien never had children. If he survived, he may have gone on to have children, which would explain how Isabel's maiden name could be Vesper-Hollingsworth, and why it stated in Into the Gauntlet that the Madrigals "had been a thorn in Isabel's family's side for centuries." (I may have misquoted, since I don't have the book with me.) Or maybe he discovered the secret to eternal (or at least prolonged) life and actually is alive in the 21st century, after all. Your theory, that the phrase in mean metaphorically, is definitely a possibility.
I have several theories regarding "The Mother was Murdered." It could refer to Olivia Cahill, since she was murdered by Damien (or, at least, his men) in Vespers Rising. It could also refer to, although less probably, Hope Cahill. Hope was murdered by Isabel Kabra, a suspected Vesper. I think this theory is unlikely, though. It could also refer to, even less probably, Grace's mother. She was implied to have died in childbirth, but maybe the Vespers had something to do with her death, and made it look like it was natural. Another possibility is, if my second theory about the meaning of "Damien is Alive" is correct, and Damien did survive and have children, he could have murdered his children's mother. He seems like the kind of guy to do that, don't you think?
Sorry about hiding so much. I have no clue how many books people reading this post will have read.