Hi Again!
It's a pretty straightforward route from Shingawa - Disneyland, the station for Disneyland is called Maihama.
From Shinagawa travel to Tokyo station and take a train from there to Maihama.
Here is the route in Hyperdia. They route is covered by the JR Pass.
All JR lines in Tokyo are covered by the JR Pass - other transport methods like the Tokyo metro don't accept the JR Pass. Here is a map from the Tokyo area with every line and station covered by the JR Pass.
I see you are already a little familiar with the route Tokyo - Fuji with a transfer at Otsuki. The route takes about 150-180 minutes assuming you travel to the Kawaguchi-ko area. You can find more about traveling to mount Fuji here.
As for traveling to Osaka/Kyoto, the JR Pass does cover this route and you can ride the bullet train there!
I hope this helps,
Daniel