Need advice on transportation

have started to plan up my trip to Japan at the end of this year and my journey will be like this:

Arrive at Osaka - Mt Koya - Iseshi - Kyoto - Takayama - Kiso valley - Nikko - Osaka to land off

Im thinking about buying JR Pass after checking out the single fares at Hyperdia, however im still want to find other railway pass or region pass or bus pass to keep some extra money for shopping.

Therefore any recommendation?

Definitely recommend reading the travel section!

A JR pass is not very useful around Osaka and Kyoto.
For Koya and Ise you should get a Kintetsu Rail Pass. It will also get you to Nagoya where you can get the JR Hida Express to Takayama.
It's good for 3 rides on Limited Express, reserved seat trains and 5 days on regular express and local trains. A real bargain.
A 7-day JR Pass might pay off for Nagoya to Takayama, Tokyo and Nikko, then back to Osaka.

what about highway bus?? i found some routes that have cheaper price than JR