Here is Yugi Muto's Deck from the Waking the Dragon Arc and the Grand Championship Arc. This deck includes all the cards that were listed in the decks Yugi used in both these arcs. The reason I combined both of these decks together was that one of the arcs' decks didn't have enough real-world cards to build a full deck without adding Anime exclusive cards, which is what I wanted to avoid. Plus, the Grand Championship arc takes place right after Waking the Dragon arc. So, it is possible that Yugi had the cards he used in the GC arc during the events of Waking the Dragon. This deck was made possible by the information on Yugi Muto's Decks page on Yugipedia.
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