Nice work, Housetek!
I've been in and out of Tokyo many times and I actually did pretty much of some of the things that you had soo painstakingly explained. Yeah, you really need to budget yourself very well in order not to find yourself running out of cash towards the end of your trip. But if you actually had more than you had planned at the end, then you can treat yourself to something nice and expensive, something that you had been avoiding all the while since the start of your trip.
One thing I want to add in here is the JR Travel Pass. You can only buy this in your country, like when you are not in Japan yet. With this travel pass, you can save quite a bit on your overall travelling expenses when in Japan. You can use this within Tokyo and even out of Tokyo.
You can use this for rail and bus.
When in Tokyo, you may want to check out the Seishun 18 pass as well.
Have fun.
