Hi Again!
I see that you have been busy ;)
I would recommend reading the Wiki travel page about traveling to Fuji as it has a lot of information available. It is always hard to give advice on what route is best to Fuji as ''Fuji'' is not just museum in one stop but consists of many areas, all with different routes. The most popular (and perhaps beautiful) area is Fuji five Lakes. Access to this area is either done by direct highway bus from Tokyo station or Shinjuku and costs 1700 yen or you can take the JR to Otsuki (covered by the JR Pass) and transfer here to the privately owned Fujikyu lines which is 1,100Yen.
To Takayama, I would simply take the bus/train back to Tokyo station, board to Shinkansen from there and travel to Takayama via a transfer at Nagoya station. Here is an example route.
As for your last question, travel time from Nagoya to Ise-shi is about 90 minutes so you can certainly do visit it for a day and make your way back to Tokyo in the evening. Just be sure to plan your day's time table ahead, so you don't get stuck somewhere!
Have a pleasant journey!
Daniel