Just re-Reading Peace Talks, page 19 states that the small wooden skull was prepared for her. Bob originally asked for it as a backup. However, many people have wondered how Bob didn’t spot Bonny growing. Perhaps the answer is he did, but didn’t tell Harry, (because he didn’t ask) but made sure Bonny had her own Sanctum when born.

This implies Bob put Bonny over Harry and was expecting Harry to die when Bonny was born, as happened on most such occasions. It also suggests that Harry has realised this. It may explain why Bob pleaded to Harry “don’t kill me” later in Battle Ground.

I don't seem to remember Bob ever "scanning" Harry, though he perhaps he sort of hints that he is able at the end of Small Favor when Harry is alarmed when Bob tells him he uses up some of his soul when he uses soul fire, then says a hug can restore it.  But can one really scan for another's soul?  Seeing Harry's soul as Bob meant it isn't the same as a soulgaze.  So I don't think he could have seen Bonea even if he was looking for her.

(1) The mug appears to be actual matter and not composed of ectoplasm, so it isn’t a common conjuration like with conjouritis. That means putting in enough energy to create the matter from scratch and that is prohibitive see e=MC 2.

Gifts from Kringle or Santa are usually made of actual matter, not ectoplasm.  In the real world you are correct about creating matter from scratch, but this is the Dresdenverse..  It is also a gift from Santa, and a bit of a miracle, and as such all practical rules of the universe to out the window.

Malcolm is a spirit, and does not possess even the ghost of the Coffee mug, but does know it’s importance to Harry without invading his mind. He may have known what happened to his stuff as a spirit. He then tells Kringle about the Mug and where it is and Kringle gets it.

Doesn't matter, even as a spirit, Malcolm is Harry's loving father, and as loving parents everywhere if asked by Kringle, would know what would comfort Harry the most.  Especially when you consider how close they were in life, it was just father and son until his death. He tells Kringle and Kringle gets his elves to put it together to present to Harry on Christmas Eve.

Harry already had Soulfire in Turn Coat. He charged up his lasso/noose with it and Shagnasty even asked him about it.

Yes, though I'd argue that beyond what Bob had told him and the boost it gave some of his spells, Harry didn't begin to understand the nature of Soul Fire till his tussle with Mother Winter in Cold Days, but I digress.

Anyway, as pointed out  Shagnasty and it's kin have been around since the beginning of time, so
it just stands to reason that it would have run into runes of that kind in the past and their effects.

There was, but he took a deliberate step down to stay in the game as a mortal, probably in exchange for Soulfire from the White God and the crafty bugger figured out to still do so and regain his immortality through the White God mandated Kringle Mantle. It’s not his immortality or the ability to wield Soulfire which makes him formidable, it’s his smarts. That’s the real edge he has over Drakul.

Where is that written? Sorry if I sound rude, I don't mean to be, I just don't remember any of that in the stories, is it WOJ?

The only other in universe example of similar spellwork is actually Castle Dresden. Perhaps the Naagloshii visited Scotland?. Is there anything in Scottish myth like Shagnasty? The Naagloshii eat the magic of wizards, maybe Shagnasty tried this with one of the former residents of the castle in Scotland and was kept locked outside until he returned to his traditional grounds.

I kind of doubt that, but if say a platoon of Naagloshii attacked the island, the Warden would bind them.. If the Naggloshii who fought Harry had been in on that fight and escaped, it would remember those runes.

  We don't know about Cowl, if it weren't for Bob, Harry, and Sue, he would have pulled off Darkhallow.. So is Cowl starborn?  What happened to him anyway? He hasn't been heard from since White Night and had given the impression of being a major player.

Just an observation.  Somebody was looking for special children and using the courts and other institutions to find them.  This has been a recurring theme in the books. Elaine was probably picked specifically because she was similar to Harry.

I agree, Justin may have been tipped off about orphans born at the right time who display talent, and proceeded to adopt them..  Actually this might have been the motivation for Malcolm's murder.
If he had lived, once Harry began to show talent, surely Malcolm would have asked his father in law for help with the boy.  That had to be prevented, so Malcolm was murdered.. Another thought, someone was paid off to lose Harry's records so Eb or Morgan wouldn't have been able to locate him with in the system, then made sure that when they were sure of his talent, that Justin would find him.  I also think that while Elaine was born at the right time, she may not have been conceived under the right conditions.