travel itinerary with 12 students

I am leading a trip with 12 u.s. college students in late May. We will stay in Tokyo 6 nights, go somewhere for 2 nights and then 6 nights in Kyoto. I am having trouble finding hotels ($100 doubles) in Tokyo and recommendations for the 2 days before Kyoto (Hakone?)

K's House Tokyo
http://kshouse.jp/tokyo-e/index.html
03-5833-0555

Sakura Hostel
http://www.sakura-hostel.co.jp/hostel_facilities.htm%20

Tokyo Hostel
http://www.tokyohostels.com/index.php
03- 3875 - 3264

Tokyo International Youth Hostel - Iidabashi
http://www.tokyo-ih.jp/
03-3235-1107
They have 2 bunks per room with lockers for your stuff. The problem for students (but not for teachers) is that they have a mongen (curfew) that is around 11 PM. You also have to be out between 9:30 AM and 3 PM while they clean.

The Toyoko Inn Asakusa Senzoku is Y9240 for a twin.
http://www.toyoko-inn.com/e_hotel/00012/index.html
The Toyoko Inns are clean inexpensive business hotels. The rooms are somewhere to sleep, and maybe catch the weather on TV while you put a beer or two in the fridge. I use them all the time.

You can also check at other Toyoko Inns around Tokyo.

As for your 2 days, check out Takayama. There's more there than in Hakone, unless you like tourist traps. Takayama has a couple of morning markets, an old house museum, and several museums on the north side of town, such as the "Float" museum for the festivals, a Lacquerware Museum, a Lions Mask Museum, and line of temples along the hillside, and old section of town, and one place has a model of Nikko for some reason. There are also a couple of merchant houses that you can go through. You can navigate the town on foot. There are some business hotels right in front of the station also.

Good luck, I may see you in May. I take a group of students starting in Hokkaido down to Kyushu for 6 weeks each summer. I stay where they stay so they rarely complain.