This one was a bit tricky to figure out because it was only showed for one duel in the original series so there were not enough cards for a full decklist, to remedy this while keeping the deck as authentic as possible I chose to go forward rather than backward, using what we were shown in GX to complete this deck, anyway my thoughtprocess probably needs a bit of explination here:
In Yu-Gi-Oh! GX we get to see Yugis deck a total of 3 times, 2 not counting Jadens graduation duel against Yugi as there was some time shananigans involved in that and Jaden ended up facing off against an earlier incarnation of Yugi, one not yet seperated from Atem, so we can just ignore cards shown in that duel,
The other two times that Yugis deck was shown was when his actual deck was "going on tour" and in the last few episodes of GX where there was a replica of Yugis deck that was to be given to the student who did the best in the graduation Duels, plus we know he had Winged Kuriboh because he gave it to Jaden in episode 1 of GX after it fell out from his deck.
I've chosen to use all the cards we saw in his actual deck and in the replica to get the best and most complete version of his final deck (not counting cards from the Dark Side of Dimensions movie because that is a continuation of the Manga, not the anime, so I'm pretty sure that's not cannon and Pyramid of light obviously takes place before Yugi and the Pharoh seperate).
Anyway since Yugis deck has a lot of bricks as it is I chose to mainly add cards that would help him play defensively and stall, and side deck the rest, but I did chose to add BLS Envoy of The Begining over Gazel or Lightforce Sword which would be better defensively because this deck could use a more reliable/easy to summon boss monster than Valkyrion or the Level monsers,
I chose to exclude the Dark Magician family of cards because Yugi not using, or drawing, any of them in his duel against the Pharoh seems to imply that he removed them from the deck or side decked them,
I could have put them in since they are shown as part of his deck later, but I prefer this thematically, the lack of any Dark Magician cards in this deck symbolising Yugi coming out of the Pharohs shadow since that really does feel more like the Pharohs ace monster than Yugis,
Plus they could just be prominantly displayed in the replica and while on tour because they are iconic, for all we know Yugi might not even use them anymore, or maybe he does, who knows :P
Anyway this has been my interpretation of Yugis final deck, I hope you like it!
P.S. the cards that were not confirmed in the final duel but I added are all the ones behind soul rope