Thank you so much for all of the help! I have booked us into the J-Hoppers Osaka (it's a hostel but there's a twin room and I've been there before, then I will stay with a friend in Otsu but we found a small hotel for my mom just up the street and I booked the Chisun Hotel Hamamatsucho in Tokyo as suggested. It ended up coming to $100 a night ai (Expedia's fees of $14/night was shocking) but it still seems like a pretty good deal.

Thanks again!