1. I think the guardian of the building was some sort of a guardian of the time: past, present and future. That's why she knows everything. But I don't think she sent Jae Woo to the past.
2-3. But there wasn't a time loop, was there? I mean, there are only a few weeks in 2022 when Jae Woo doesn't "exist" and there are two in 2007. The time flew just the same and there weren't overlaps.
4. I think they didn't a great job with the make-up. I didn't look at it so carefully, though, and I don't know if it hints about something else...
5. Yes, there were many but I'm glad that the authors kept the past exactly the same as in our timeline. Another solution could be that the three boys went to take little Jae Woo from wherever he was and accompanied him home making another route. And even if they bumped onto the kidnapper, they were three young men against one man with a knife.
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I just realised replying to your questions that there's a few weeks hole in 2022 where there's no Jae Woo. That's probably what Ji Hoon meant that JW could meet him every 15 years? You have any idea? The letter mentioned a third meeting between them...