Yes, please do give shout out of any places, it'll be my first visit to Japan.
Im definitely keen on shopping for equipment, I'll be going to most of the big shopping department/area. Can you suggest any dedicated aquascaping stores?
I'll be in Tokyo for a week then train down to Osaka and spend the remaining time there and fly home from there too, so a JR wont be necessary.
I'll bring back shrimps......; any shrimp favoured food products I can find!
For aquarium related shopping, check out any of these stores; I am not sure where you are staying in Tokyo, but they have a maps too...
They all sell ADA equipment to some degree or another. I particularly liked Penguin Village, Pau Pau Aquarium Garden and Aqua Forest.
You may or may not find people that speak English. I speak Japanese, so it wasn't a problem...
It is too bad it is difficult to bring back livestock/plants/electrical equipment (North America is 110/120V at 60 Hz, in Japan it is 100/110V at either 60 Hz or 50 Hz, depending on Kanto/Kansai region, respectively).
The cheapest way to go from Tokyo to Osaka is by night bus (2300 yen!), but with luggage it is a hassle. Taking local trains is out of the question (takes maybe 6-8 hours?), so your options are pretty limited (shinkansen, airplane, etc)
Here is a list of things to do, just off the top of my head, in no particular order.
Akihabara (Electronics, anime)
Kappabashi-dori (Kitchen town, they have kitchen gadgets, the plastic food samples that you will inevitably see in restaurant display windows)
Shinjuku (the area in general; Kabuki-cho (red-light/entertainment district))
Shibuya scramble crossing, Hachiko statue, Shibuya 109 (upscale shopping mall)
Harajuku (Take[censored][censored][censored][censored]a dori, Omotesando dori; pop fashion and high fashion, respectively)
Tokyo Metropolitan buildings (you can go to the 50th floor to get a view of the cityscape for free)
Roppongi (clubbing, night life)
Tokyo Disney Land
Namba (shopping, Glico man)
Nipponbashi (electronics, anime)
Osaka Castle/surrounding park
Osaka Kaiyuukan (aquarium)
Universal Studios Japan
Kinkaku-ji (Golden Pavillion)
Shimogamo and Kamigamo shrine
Kyoto Imperial Palace
Uji (Byodo-in; temple (the one on the back of the 10 yen coin))
From Osaka, you can make a day trip to Kobe, Himeji (unfortunately the castle is under construction), and Nara (Todaiji temple, Nara Park).
If there's anything in particular you're interested in, feel free to ask.