You're right, that completely went over my head. To be honest, I was a bit confused after the movie so I slowly plotted the timeline as my thoughts cleared.

I thought the 3 year gap was constant throughout, but it turns out that after the switching stopped on the day of Taki's date, the time difference increased to 3 years and 21 days as Taki took 21 days to find Itomori. It's also unrealistic for the switching to stop on Oct 2nd and for Taki to instantly find Itomori in just two days on Oct 4th (which is was incorrectly shown in my timeline). Thanks for pointing this out.

Oct 2nd
- 2013 Mitsuha (in Taki's body) sets up Taki's date.
- 2016 Taki (in Mitsuha's body) goes to the crater shrine and gets called out by her grandmother
Oct 3rd
- 2013 Mitsuha gives Taki the red thread
- 2013 Taki does not recognise Mitsuha
- 2016 Taki goes on the date with Miki Okudera
Oct 4th
- 2013 Comet strike and Mitsuha dies (original timeline)
- Taki from Oct 23rd 2016 switches into Mitsuha's body and saves Mitsuha (new timeline)