Re: Deadly Blow...
First, to answer the actual question: to be legal, either the Deadly Blow damage gets applied separately from the AP damage, unless you buy Deadly Blow with the Advantage. (Pro-rating makes sense and I'd probably do it, though it's not really legal book-wise.)
However, my opinion is that Deadly Blow is illegal because the Hero rules prohibit you from buying an attack power that adds directly to any other attack power you pick up. If I allowed it in a game, I'd rebuild it as buying the entire KA from scratch with OIF (Weapon of Opportunity), or as an Aid, either of which would make the cost more appropriate.