Hello jjtsang ^_^
I have booked room in share house in Nishi-Shinjuku and i will move in it in september, the same house have two room available right now with the same budget you have in a perfect location, even one of the room with balcony.
Here is the website where you can check photos , price, location even the gender and nationality of the people living in the house.
The best thing i like in this agency that they dont ask for deposit, key money or anything like this , just management fee of 20000¥
Hope this link will be useful to you and others :)
All the best
Thank you so much for the info! But I'll be living here long term so I'm actually looking to share an apartment with just a 2-3 roommates instead of a guesthouse. I appreciate your advice though and I'm sure it would be of great help for someone else here!