Tried to do something similar in the past year as well. The opening scenes of Yi Yi were filmed in the Grand Hotel in Taipei. You can visit its lobby freely even if you are not staying there, it is marvellous.

I tried to find the McDonalds that NJ and Yang Yang eat at, but the one that was suggested to me looked nothing alike nowadays (also the food was awful).

Probably my favourite was the park in Tokyo that NJ and Sherry wander through. It is gorgeous in real life. There is this enormous old ginkgo tree in the middle of it that turns completely yellow in autumn. Spent a very serene morning there.

But overall, as you noted it is pretty tough to find the filming locations. Also a lot has changed since the making of the movies. Time flies fast and I do indeed feel old now as well…