This is great, thanks for the input. I'll be sure to do further research into these places.
Let me know (you can either post here or PM me) if you want more details regarding some of the places. I know that the ADA link that I provided earlier was in Japanese, but if you click around, you should be able to find the map, etc.
If there are several that you are particularly interested in, I can do a little digging to give you the precise address/maps/telephone numbers/whatever.
2300 YEN Bus from Tokyo to Osaka is crazy cheap! But im willing to pay extra for a Shinkansen train ride experience!
Yes. Though for the price, you have to sit on a bus for 6-7 hours. And it's a night bus (you board around 11 pm - 12 am, then arrive around 6 am), so that might turn some people off. I had no problems and just slept the entire way.
Shinkansen from Shinagawa to Shin-Osaka stations costs ~14000 JPY, which at today's market rate is ~170 USD. It takes approximately 2 hours and 20 minutes.
Can you suggest the best method for foreigners buying mobile communication and internet data? Ideally, I want to buy a SIM with internet data and use my Apple iPhone for map navigation and calls. But I hear its quite different over there, you'll need to buy both Phone and plan? And Free Wi-Fi hotspot is scarce.
There are several ways to get a cell phone (with data) in Japan...
Strictly speaking, the easiest way is to go to a phone rental shop (they are usually in the airport). Docomo, Au and Softbank are your three choices, but Softbank is probably going to be the cheapest (of the three). Rental fees (and your subsequent usage) can be expensive.
Prepaid plans are available too, but this usually
requires proof of residence in Japan, so if you have a tourist visa, you usually
cannot get them. There are "gray" markets that are available where you might be able to get them, but...
So in general, your best bet is to get a rental phone. But, as mentioned, they might not have data. If you want a smart phone with data, it'll cost (more) money. They should have English, so not to worry about language preferences. Though the maps will all be in Japanese, so you might just want to research where you want to go, and print out all the maps.
Wi-fi was scarce, but is becoming increasingly more common. Starbucks, McDonald's and some coffee shops (Ogawa Coffee, etc) usually have free wi-fi now.
Edit: I edited my list of places above as well. Some more places popped into my mind.