Hi there!
I see that you have already been thinking a lot regarding your upcoming travels and it is good to see that you've already made a list with what you wish to see and visit. This makes planning and finding good recommendations a lot easier.
Still Japan has a lot to offer and making a finial selection may be hard.
Okay, let's jump right in and have a look at JR Passes and other ways to get around. First I think that a 7 day JR Pass combined with local tickets in Tokyo and Osaka is the best option, especially if you wish to see multiple cities in Japan. For local travel in Tokyo and Osaka, I would recommend getting a so called IC card.. Assuming that you arrive at Narita Airport, consider buying [Suica + N'EX] package. This is a discounted ticket on the Narita Express directly to Tokyo station as well as a SUICA IC card which you can use to pay for your local travel around Tokyo and later in Osaka as well.
On to your 7 days of JR Pass usage, the main idea would be to see as much as possible within 7 days and arrive in Osaka on the last day, so you would have all of your long distance and pricey train traveled covered by the JR Pass.
You could think of the following itinerary:
Stay in Tokyo
Day 1 - 3 Stay in Tokyo, visit Tsukiji Market (good idea to do on the first night if you have a jet lag), maybe stay at a Capsule Hotel and or Love Hotel at Love Hotel Hill located near to Shibuya. Note that many capsule hotels only cater to business men and females are often not allowed to stay in a Capsule hotel. I stayed at Kanda Value Capsule Inn this summer and they women can stay on Sunday and Monday nights, in addition there Shinjuku branch as a women's floor available for 7 days a week.
Starting the JR Adventure
Day 4, Start using the JR Pass. A great prace to start would be traveling to Matsumoto the castle there is one of the best in Japan, in addition there are some great hiking opportunities around such as a visit to Kamikochi. I would recommend staying here 1-2 nights.
Day 6, A great place to visit next is Takayama, which is a beautiful traditional village, also well known for it's beautiful autumn leaves. This train ride is very scenic because the train track follows a river that comes down trough the Japanese inland mountains. The route can take a good amount of time though, so I would recommend bringing a good book to read as well.
Close to Takayama, you can find Gero Onsen where you could drop by to enjoy an onsen or two.
Day 7-8 From Takayama there's a couple of options that I would recommend considering. The first is going to Kyoto, the traditional capital of Japan, with many interesting places and attractions to see. Some of the best include Kiyomizu-dera, Fushimi Inari and a hike around Kurama.
An other option would be to go up to Matsue and Izumo. Some of the most beautiful things to visit here are the Adachi museam of art and zen garden in addition to the Izomo Taisha Grand Shrine.
Yen an other option would be to head to Kinosaki-Onsen to the north of Kyoto. This is a very lovely Onsen town and has some amazing Ryokan where you can stay the night. You can visit this town as a day trip from Kyoto but it is best to stay the night here.
Day 9-10. Before heading to Osaka, I would recommend a visit to Hiroshima, where you can visit the Peace Memorial Museum and park, in a addition to a trip to Miyajima which is not to be missed on any trip.
On day 10 head to Osaka, as this is the last day of your JR Pass. You could make a stop at Himeji on the way there and visit the Castle and gardens. You could do this in 2-3 hours, so it won't take up all of your day.
Day 11-12. Sightseeing around Osaka, my personal recommendations would be a visit to Shinsaibashi and Namba. Here you can really feel the atmosphere of the heart of Osaka. I would recommend taking a look at this website for more information about Osaka.
All places are covered by the JR Pass, including the ferry to Miyajima.
I have pinned all places mentioned above to this map for you so you can get a feel for the distances and train lines involved.
I hope this gives you an idea of the possibilities!
-Daniel
PS: It's interesting that you mention the Autemn leave viewing or kouyou, the characters are 紅葉 and can be pronounced as either kouyou or momiji, the last also meats maple leaves.