You could live for two months on $3k if you were staying at a gaijin-house type dormitory, and there are plenty of such places located around the city.

Prices vary dramatically in the city depending on location. You can rent a 3 or 4 house in Nerima-ku for 150k yen, but that much won't even get you a studio in Chuo-ku. Outside the city the rents get even cheaper; my 3 room house in Chiba is only 60k yen per month, whereas my GF's 3 room apartment in Shinkawa cost more than 5 times that much.

There are apartment buildings in Roppongi Hills which rent large apartments for 3 million yen per month ($30,000). A penthouse apartment will cost quite a bit more than that.

They have boards that have studios for rent all over Tokyo.
The prices are reasonable as well.

The rent prices might seem reasonable, but you then have to figure in move-in costs. A couple months refundable deposit, and 1 to 3 months of "key money", which is not refundable. Your 90k yen studio could cost as much as 500k yen to move in. I had to pay the equivalent of 3 months rent in addition to my first month's rent, meaning that my move-in cost was about 250k yen. Not cheap.

$2,000 you can live on but with $3,000 you'll be a lot more comfortable.

The question I always ask...why move to a foreign country to live like a hobo?

Yes the deposits are really the biggest downside to renting in Japan.
I think it's just a little too much money up front.

and it's a damn good question !

It was something I definitely took to heart during my trip planning.

Maybe to experience something different? Maybe because it sounds challenging or adventurous?

If you want to experience a different country or culture, I'd imagine that you'd learn the most by living at their average living standards.

There isn't much to gain by learning how the poor scrape by in a foreign country.

Nobody, at least not me. Want to live like a hobo. Thats why I'm asking the question about price. I'm assuming $5,000 would be a bit more comfortable. In the end, I want a fun experience not a struggling one. :D