Itinerary for Japan the second time around

Hi everybody,

I'm going back to Japan in July. Huzzah! I've already visited the main sights of Tokyo, Kyoto, Nikko, Nara, Hakone and Mount Fuji. So I'm considering the following itinerary. Keep in mind that I'm dependant on public transport and my budget is limited. Tips on things to see / things that aren't really worth it, absolutely stuff I must try, cheap places to stay, etc are always welcome!

Day 1 Tokyo: parasite museum, eat shabu shabu, go to onsen, sleep in capsule
Dag 2: Tsujiki fish market, cooking class, meeting with friend, karaoke, try another capsule
Day 3: daytrip to Ito Island (Iza peninsula) to see Mt Omuro and Jogasaki, return to Tokyo or travel on to Nagayoma (can you travel on or do I need to return to Tokyo?)
Day 4: Nagayoma (Nagoya-jo castle,Tokygawa-en garden, maybe no-theatre if budget allows) , go to Nagoya (is this possible?)
Day 5: Inuyama (Inuyama-jo castle, Kiso-gawa fishing), return to Nagoya or travel on to Takayama (is this possible?)
Day 6: travel to Takayama (Karakuri museum, hida folk museum, eat hida beef) , stay in zenko-ji temple if possible
Day 7: travel to Matsumoto (is this possible, not sure that I want to go there yet. Anybody who can tell me if this is worth the visit?), stay there or go to Kyoto (possible?)
Day 8: Kyoto: gion, philosophers path, karaoke!, capsule ryokan
Day 9: Himeji castle, return to Kyoto for Gion matsuri

Then return to home. I still have to figure out where to in/fly out of Japan depending on ticket prices and smart use of the JR pass. Reversing the route (ending in Tokyo and starting in Kyoto) is also an option.

Thanks for your advice!

Japan   Tokyo   Ito   Takayama   Matsumoto   Kyoto