Hi Timmo,
Sorry for the delay in response, I had not forgotten it but had to find a moment to sit down and research.
Going into your route.
Kyoto - > Kanazawa: Fully covered by the JR Pass, you can use the Thunderbird express for the fastest route.
Kanazawa - Uozu: Take the TSURUGI Shinkansen from Kanazawa to Toyama and from there the Ainokaze Toyama Railway to Uozo. This last part requires ¥560 fare.
Uozu - Nagano: take the Ainokaze Toyama Railway back to Toyama (again 560yen) and then the Shinkansen to Nagano.
Nagano - Fujinomiya: Fully covered by the JR Pass. Take the Shinkansen to Tokyo, then a combination of the Tokaido Shinkansen and local JR lines to Fujinomiya.
Fujinomiya - Ise: fully covered but be sure to use JR lines between Nagoya - Ise and not the Kintetsu lines.
Ise - Osaka: Take local JR lines back to Nagoya station and from there the Shinkansen to Osaka.
As you can see the only addition fare is to and from Uozu.
Hope this helps,
Daniel