Hi Faisel,
Here are some answers:
Can someone tell me if the rail pass will cover all the transport needed to get to these destinations or have a link to a website where I can plan this trip out with timetables etc?
The best source of timetable information for JR trains is www.hyperdia.com. We also have a video showing how to use it for JR Pass holders on our blog.
On your itinerary:
Train from Tokyo to Hiroshima
Yes - this is covered with a JRPass on all trains/bullet trains (itinerary)
Train from Hiroshima to Kyoto
Yes - this is covered with a JRPass on all trains/bullet trains (itinerary)
Train/bus to Shirakawa-go
To get to Shirakawa-go, you'll first want to get to Takayama by JR trains and bullet trains, which is simple to get to from Kyoto (Here's the itinerary).
Once in Takayama, you can easily get a bus to Shirakawa-go from the Takayama Nohi Bus centre, which is a short walk from the station. At 50 mins, the bus journey is quite short so you should be able to incorporate Shirakawa-go into a day trip from Takayama. Please be aware that this bus is not operated by JR and so you will have to buy separate tickets (¥4,300 round trip). You can find timetable information on this bus at the [Nohi Bus online english timetable].
Train/bus back to Tokyo
Your return to Tokyo from Takayama is fully covered by the rail pass. Here's a sample itinerary for you.
Hope this helps!