JR pass using Hyperdia

Hi,
I am building our train schedule for 21 day travel in Japan using Hyperdia and have some question regarding JR trains. I am considering buying JR general pass

1. How do I know which trains are covered by JR pass. I see some marked as JR - are these the ones that are covered?

2. Can I assume that all bullet trains are covered with an exception of NOZOMI” and “MIZUHO

3. If my route has a combination of JR train and the train not covered by JR pass, I assume I need to buy the ticket for not covered route. Can I buy the ticket in Tokyo?

4. In many cases it is not clear how much is a ticker for a not covered route.

Here is an example from Hakone to Takayma: I can see 310Y fare for Tozan Raiway and 7,569Y from Nagoya to Takayma. I don't see the fare for Shinkansen Hikari from Odawara to Nagoya. I assume JR pass covers it, but if I don't get the pass, what would be the fare? Or am I not reading correctly and 7,560Y covers Odawara to Takayma route (includes shinkansen fare). In this case is 7,560Y covered by JR pass.

Route1 Take time: 269 Minutes Transfer: 2 Times Distance: 454.9 km

Total:¥ 12,450(TicketFare:¥ 7,870 Seat Fee:¥ 4,580)

Time Route Fare
09:39 begin HAKONE-YUMOTO

             Hakone Tozan Railway  for ODAWARA        ¥310           09:53 10:08
             transfer   ODAWARA 

[69 Min] through SHINKANSEN HIKARI 507 11:17
11:43 transfer NAGOYA ¥7,560

[145 Min] through LTD. EXP (WIDE VIEW) HIDA 9

14:08
end TAKAYAMA

Thank you so much for your help!
Maria