well i checked in for my first 2 weeks in the
Economy Backpackers Hotel NEW KOYO . I dont know how it will look like, but the page looks ok and it runs at 2500-2700 Yen a night. Its bassicly like a Hostel with shared bathroom and kitchen, but with single rooms on the price from normal Hostel rooms. It is in Ueno, so it might be a little bit off the spot for you, just check it out. Note that the rooms are really small i guess, but for me thats not a problem, at least i have my own room.