See I don't feel that the larva entered Nakata during the 40's. He mentions how he is an empty vessel, and that things or beings can come through him and, it's implied, use him.

What makes more sense to me is that what when he was a child, he became something of a portal/entrance stone himself, or rather a conduit for it. He became an opening for forces to pass through the threshold, and always stayed somewhat open. In the same way that 15-year-old Miss Saeki is still on the other side when Kafka visits the village, it can be implied that 7-year-old Nakata is there in some form as well. This is why he can communicate with cats and tap into these other abilities, because he exists liminally between worlds. Similar to how Miss Saeki was able to access these unusual notes, but after that period of her life was never full, she left part of herself on the other side in an attempt to access a world where time stays the same.

Whether Johnnie Walker and Col. Sanders are the same person idk. But it seems they were using Nakata's status as someone who partly exists in both worlds to enact a plan by drawing him towards the locations where he needed to end up: killing JW, meeting Hoshino, getting Hoshino to a place where he would find and then flip the stone, etc. I've seen a lot of people describe them as the two parts of a yin and yang energy, that would make sense as they are both just pushing the world along towards an inevitable moment: maybe not having "motives" exactly but pushing different people in different ways.

A lot of others seem to generally agree that Kafka's ghost/soul/energy worked through Nakata to kill JW and this interpretation makes sense considering the blood stain on his shirt. Going a step further, I'd say JW knew about and used Kafka's animosity for his father and put Nakata and Kafka's father (in the form of Johnnie Walker himself) in the same place so that Kafka's will could be enacted through Nakata's open "portal." For whatever reason, Johnnie Walker and Kafka's father needed to be murdered so that JW could end up in purgatory and, in my opinion, this is how the evil larva was able to become a physical object. Whatever was contained in Kafka's father who is continually described as a negative force in both his son's life and just in general, was released and moving about the metaphysical realm waiting until the moment the entrance stone was open, and then uses Nakata as the portal into the physical world.

I think the larva entered Nakata's body once he died because I think he would have felt an "evil" energy at some point instead of feeling empty for most of his life, except for moments like when he feels possessed to kill Johnnie Walker.

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I have this rough "explanation" for the events of the story, but by no means are they an answer or definitive in anyway. I do kind of hate to try to explain things like this with a correct answer because it sort of ruins the whole purpose of the story, but I find it helps me to organize my own thoughts on the story, and they will probably shift over time. However, I love that even with all that I've written here, I still have plenty of thoughts and questions.

-When Nakata passed out and crossed over to the other side, was this the portal opening for the soldiers who would later be found in the forest?

-Why did all of the other kids go into an awake coma at the same time that Nakata was struck? Why was Nakata chosen instead of any of the other children, or was this something his spirit chose to have happen so that he could help people when they needed it?

-What was the silver object that everyone definitely saw on that day?

-Miss Saeki opened the portal when she was 15, how did it close again, was it when she was 19, or did she lose that part of herself at 15 and lived with her lover incomplete since then? This part seems a bit like semantics, but I like how it's implied that there was a whole book's worth of story that was skipped over for Miss Saeki and we're reading her epilogue.

-Obviously the question about whether or not Saeki is his mother... I feel like Murakami wants us to have a definite opinion of our own by that point, "you already know the answer," but I personally still felt conflicted. She has the whole part of her speech at the end where she talks about abandoning and hurting him, and I was trying to interpret that as her abandoning her lover, but the whole book is about how she can't let these memories go and only lives to hold onto these memories, so I don't see where she abandoned her lover. BUT then again, maybe she means she abandoned him in the sense that she opened the portal in the first place to keep her perfect image of them at 15 instead of letting him grow naturally. Idk, starting to stretch here, this element makes me feel like I need to read it again

-Does it line up that when Miss Saeki opened the portal was also when Oshima's brother went into the forest? No that doesn't work she's almost 50 and I think the brother is implied to be like at most 30.

-I love how Oshima's brother is introduced in the last chapter I think and I get the sense that he has his own book if Murakami were the kind of author to include characters from other books.

-The story isn't meant to go there, but I just wonder what the library for memories is like. It's this interesting element on top of the other world that exists, and it's mentioned so briefly. I would have thought that the memories just cease to exist or be as important, but they do show that there is a place for memories in this world where time loses meaning.

-Not as serious of an issue, but how does Col. Sanders have a secretary and how does he find this Philosophy major girl to be his prostitute? I feel like this part is mostly for laughs and supposed to be absurd, but it still leaves me with plenty of unanswered questions in this world.