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Just as the little implies, in Kaitou's vol 4 or the anime adaption, Shinichi is shown having a confrontation with KID BEFORE turning into Conan, but in his first DC appearance Conan seems to have no previous Knowledge of KID. Also the org Kid is competing against (be it the BO as suggested by some people or another) hasn't make a single appearance outside an OVA. Is the KID from DC the same from Magic Kaito and Gosho simply neglected to think or add those details or a different one added only as a "filler" in DC?

READ THIS HEHEH

Shinichi never exactly saw Kaito at the clock tower, and it's unclear how much he knew about the thief; he seemed to recognize the name when Agasa said it, though.
The relationship, if any, between Snake's snipers and the BO is unknown. Possibly they're the same lot, given their shared obsession with immortality and the lack of apparent criminal turf war. Possibly not.
But it is the same guy. He was seen with Aoko in his first appearance, and Hakuba's still hunting him. Nakamori-keibu's chasing him too. The only MK regulars not to have appeared in MC are Keiko and Akako (Jii's face isn't shown but it's almost certain that he appeared in the Walking on Air and Teleportation heists). He also appeared as a child with Toichi in a flashback. The same guy, it's just that Aoyama hasn't woven a lot of MK storyline into DC yet. He said he might, though. The most we've got is Kid continually saying "it's not the jewel i'm looking for".

Everything is canon outside of silly stuff involving magic or robots.

I think if we ever get some major Kid arc (which I hope we do), it would be interesting if they have magic in that arc, but only Kid and other Magic Kaito characters have anything to do with it.

Akako would severely mess with Shinichi's head. She's about the opposite of logical.

At the end of the clock tower case, Shinichi says to Megure-keibu:

"Oh yeah, you never told me did you? The name of that theif..."

But then, Megure was so into trying to solve Kaito's code that Shinichi gave up trying to ask. And during the case, Shinichi always refferred to Kaito as "that thief" because he didn't know what to call him!
And then, like I said in like 2 other threads, Aoyama-sensei said that Kaitou KID is the same in both DC and MK... But he hasn't really clarified whether or not the organization is the same. He even said that (rough translation from memory) "Kaito was originally supposed to be just a quick, one case, guest character like Heiji was... I really just wanted a good rival for Conan actually; Heiji and him are rivals, but they're both detectives. But it turns out that he's so popular, so I like to stick him in once in a while. And it's so fun to see Conan and Kaito go against each other!"