Help with 3 Week July Itinerary

Below are my ideas for an itinerary in Japan. Some things I'm struggling with; I am realizing how far and costly it is to travel to Hokkaido and am contemplating whether to skip it. I've been told by numerous people that it's a great time to go as everywhere else is humid and rainy and hot. Should I leave it in or take it out? Otaru does look great but getting around Hokkaido seems difficult.

i'm also contemplating skipping Mt Fuji; is it worth the climb if we don't head out at midinight to catch sunrise? Same with Hakone; I feel like the only attraction is seeing Mt Fuji from afar. I thought instead I could go to Takayama and Shirakawa.

I also recently found postings on Izu peninsula and wonder if I can fit it in somewhere; perhaps if I skipped Hokkaido?

A little background; I'll be traveling with my boyfriend (ages 30 and 31) and we like food, esp Japanese food (yakitori, ramen/udon/soba, sushi for sure, shabu shabu just to name a few)... we also like japanese art/ culture incl contemporary arts, watch a fair amount of anime. My boyfriend is also a huge animal lover (small and large). I enjoy hiking and outdoor/ natural beauty.

We had hoped to watch Muscle Musical but realize now that they stop running in June; are there any similar shows? [We're big fans of Sasuke/ Ninja Warrior] http://www.musclemusical.com/english/

For Tokyo I hope to be convenient to a train and in the city centre but realize the trains are difficult to figure out; i want to go to Ghibli museum, maybe Muscle Park, go to tsukiji fish market, Akiharaba, Shibuya, Takeshita Street... but not sure what's convenient to these places..

Also not sure if we can get away with a 14d Railpass or just get 21d...

I know it's a lot of questions but any help would be appreciated!

Jul7 arrive NRT 4:20pm
Jul8 Tokyo1 morning at tsukiji maket, ginza?, ueno? muscle park
Jul9 Tokyo2 Akiharaba, Shibuya, Takeshita Street
Jul10 Tokyo3 Ghibli museum...... ?time for a baseball game at Tokyo dome?
Jul11 Sapporo1
Jul12 Sapporo/Otaru2
Jul13 Sapporo/Otaru3
Jul14 Sapporo/Lake Toya
Jul15 sapporo5
Jul16 mt fuji/ hakone vs takayama and shirakawa
Jul17 nagoya for sumo show
Jul18 kyoto1
Jul19 kyoto2
Jul20 kyoto3/
Jul21 kyoto4/nara
Jul22 mount koya? *solar eclipse around 11am
Jul/23 osaka
Jul24 osaka
Jul25 hiroshima1
Jul26 hiroshima2/ Miyajima
Jul27 fukuoka/ yufuin
Jul28 fukuoka/yufuin
Jul29 fukuoka
Jul30 fukuoka
7/31 FLIGHT 10:10am FUK

If you can get an air pass, Hokkaido is not expensive to access:
http://www.japan-guide.com/e/e5306.html

The Muscle Musical starts again from July 18:
http://www.musclemusical.com/guide/09summer/index.html

Tokyo transportation is not as complicated as the network looks like:
http://www.japan-guide.com/e/e2017.html

thanks for info - maybe i'll fly out of hokkaido...

hm.. muscle musical's not looking like it'll fit well into my schedule.. bummer...

Looks like you have a pretty good itinerary, leaving a lot of time in each place and not running around like crazy like some people do. I was in Japan for 3 weeks two years ago, and went to many place between Sendai and Hiroshima/Miyajima. I went in the spring, but I also have heard that going to Hokkaido in the summer is good, because its a break from the hot/humid weather of most of Japan. If you get an air pass and travel there by air as Uji suggests, you could get by easily on a 14 day rail pass. You wouldn't need a rail pass for traveling around Tokyo, or even going to Mt. Fuji. It would be cheaper to get individual tickets. You could activate your rail pass in Tokyo (after getting back from Hokkaido) on July 17th when you head out to Nagoya. Then, since you are flying out from Fukuoka, you would not need to get back to Tokyo by rail.

I would not even think about skipping Hokkaido. There are many beautiful natural places up there, not to mention the weather being better.

As for Mt. Fuji, I'm not sure if you left enough time to climb it, but if you want to see it up close, you should travel to Fuji Five Lakes from Tokyo as a day trip. I did this and went up the cable car near Lake Kawaguchiko, and then went closer to Mt. Fuji by bus and went in Bat Cave, Ice Cave, and Wind Cave (all lava tube caves, very fun). I also hiked around Ice Cave at the base of the mountain. Very pretty.

As for train travel in Tokyo, I don't know where you heard it being confusing. It's actually super easy, with signs in English, and the main train line being a big loop (Yamanote Line), plus the Chuo Line that connects the loop in the middle. You could practically get by in Tokyo as a tourist by just using those two train lines (I did). It's very easy to get to all the places you mentioned in Tokyo. Don't worry about that. I highly highly highly recommend buying Tokyo City Atlas: A Bilingual Guide, and Japan Atlas: A Bilingual Guide, along with Streetwise Tokyo map and Time Out guide to Tokyo, along with Lonely Planet Japan. Good luck and if you having any more questions, just post them here.