not yet book hotel cos confuse with the Transport route hope to finish Osaka, Kyoto and Kobe last.
please advise.
Decide how many days you want to stay in each area first.
9D for 6 areas is a little tight, unless you wish to do touch-and-go and not coming back to Japan again. Flying into Nagoya and out from Osaka would be better - no need to make a loop.
Why not just stick to Kansai - Osaka/ Kyoto/ Kobe/ Himeji if this was your first visit to the West? Save more time from traveling and money from buying expensive passes, you’ll probably enjoy more.
You can access Shirakawa-go from either Takayama or Kanazawa.
Kyoto is directly connected to Kanazawa via Limited Express Thunderbird. Are you using a Pass? Are you comfortable with taking express buses if you’re not using any train pass?
The issue now is how you would travel to Kanazawa or Takayama from Osaka. Either you take an express bus directly (provided you could reach the bus stop on time after touching down) or stay overnight in Osaka then make your way over Kanazawa/ Takayama in the morning.
Bus timetable for Osaka/ Kyoto <-> Takayama (take note of arrival time)
https://www.nouhibus.co.jp/highwaybus/osaka_en/#timetable
Kobe can be a day trip from Osaka.