I wrote an article given a bit of information for travelling Aikidoka who wish to train at hombu
. Should be a good place to start for planing your stay in Tokyo as regards to places to stay and how to deal with the whole hombu dojo thing.
About which class you should attend, try downstairs first (many advanced students also go there anyway) and if you feel comfortable enough, move to the regular dojo.
Not directly related but I also wrote something on the current food safety situation in Japan
so it might be relevant to you too
You'll have a lot of fun in Japan!