For instance: upon re-reading for the third time or so, it occurred to me that John and Rodney probably separated/broke up after the wedding and were only reunited after the assassination attempt; it would explain John being incapable of looking at Rodney when he goes to visit him in the infirmary as well as other little details.

Hmm. I hadn't thought of that. I thought their reconciliation was in the morning after, where Rodney thought (and I agree, with qualifiers) that the sex was less about John and Teyla and more about the hugeness of John committing his life to (aka marrying) Atlantis (and Pegasus).

Intereting. I need to read it with that in mind and see.