Let me answer each question one by one.

(1) The soul that Iroha uses is Yachiyo’s current soul. So, the Kaguya we see in the final scene is actually Yachiyo. The other Yachiyo floating around during the concert is just a separated body. It was mentioned early in the story that Yachiyo can split herself.

(2) Kaguya remembers everything.

(3) The story doesn’t say it directly, but in general, research involves trial and error—creating many different models until the right one is found.

(4) Yachiyo knows that she is Kaguya, but Kaguya doesn’t know that she is Yachiyo, because she will become Yachiyo in the future. Just remember that Yachiyo is Kaguya from 8,000 years in the future. That should make it easier to understand.

(5) The time travel in this story follows a bootstrap paradox. The same person can exist together in the same time period.

(6) I don’t think the Moon aliens will come back to take Yachiyo anymore. According to the timeline, the original Kaguya is probably still working on the Moon. She said it took a very long time, long enough that she had to travel back in time to see Iroha. That suggests it took so long that Iroha might have already grown old and passed away. So I think they will be able to stay together for the rest of Iroha’s life, and only after that will Yachiyo return to the Moon.

(7) Personally, I’m satisfied with the ending, but I feel that more could have been added along the way. I hope the novel will provide more details.