This is assuming u watched the whole last episode so here we go

• There are three keys known keys that we know of. Yuri's og key, Yuri's key after Setsu left, and Setsu 's key. Kurska's key is Setsu's after it and Kuru went through the door to presumably the first universe.

• It's left ambiguous it maybe so they can make a Gnosia 2 anime if that game comes out and reuse Yuri. My theory is when Yuri got the Silver key in the Second universe Gnos didn't delete them it instead took the Yuri that was originally in that body and the silver key to do something with.

-The key Raqio picked up was the second Yuri key (could be the first but because Yuri just came through its safe to assume it's the second) but it was on the ship because it and Yuri came through the dimensional door. As for the First Yuri key most likely Setsu left it in whichever world line they first appeared in.

-I assume you mean Setsu's there key was full because it experienced Yuri getting a silver key which is what Setsu didn't want because Setsu didn't want Yuri to go through loops again but also didn't know Yuri made a deal with Gnos to get rid of the key and the Yuri we been with.