This story is discontinued, but a Redux version is up called Yugioh ZexArc-V:Flowing Journey. I felt the original had way too many ideas within it, I was far too eager to have characters switch decks around, and truly connecting it to another story was the wrong move. Now, this story is better contained, characters will be sticking with decks and merely upgrading them, and this story is no longer connected to Konoha Shinobi Deck.
I'll even go a step further by outlining the three big things I want to do with the redux version:
1. Keep people switching decks low.
2. Make sure people know this is a crossover between Yugioh Zexal and Yugioh Arc-V.
3. Keep the number of OC's low. This doesn't mean I'm not open to them from other people, but I personally put way too many in the first story.
So yeah, if you want to see this story eventually reach a conclusion, it'll be in Yugioh ZexArc-V:Flowing Journey.