I'm posting my 'report' on where to find Transformers toys in Tokyo and hope it will be helpful to anyone visiting Japan for Transformers.
Full report on where I went and which toy places have G1 Transformers are in the following chapters below (too many pics to post here).
Chapter 1: In which the purpose is unveiled
Chapter 2: In which we visit the Mandarake Complex
Chapter 3: In which we visit Mandarake (Shibuya)
Chapter 4: Mandarake Complex Akihabara Redux
Chapter 5: In which we visit Mandarake Nakano
Chapter 6: The Acquisitions
Chapter 7: The Japan January 2010 "Best Of" Tally
***
These are what I bought from my trip.

Video of lots of G1 Transformers in a Mandarake shop: http://good-times.webshots.com/video/3099417180100811158TvcgKs