Seriously? That sounds awesome. I can get into lots of trouble in Aoyama and Daikanyama. Must check out Harajuka Station also. But fuck, that place so big it just depends on how much traveling you want to do and what clothing lines you are into.
If it were me, I would write down a list of places you have to go shop in and write down addresses and plan to stay in those areas unless you plan to do lots of traveling around. But if you don't plan very carefully you can burn out quickly. That place is so fucking huge and people are everywhere. It can be a bit of shock if you're not somewhat prepared.
Ah ... sorry, I don't know where Real Japan Blue and Flathead are. Do you want to visit the retail store or where they are made? I think most of that Japanese denim is made or coming out of Osaka and Okayama, which is would be several hours from where you will be, but I could be wrong. But I am sure they have retail stores all around. Maybe check the websites?