From Takayama to Kyoto

Is there a train or highway bus that goes into Kyoto city from Takayama (not drop off from the highway)?

Since I cannot find one, I have altered my itinerary to take Nohi bus from Takayama to Shirakawa Go to Kanazawa ...

Dep 12:50 Takayama NBC #2
Arr13:40 Shirakawa-go (50 min)
Dep 16:50 Shirakawa-go
Arr 18:05 Kanazawa (1hr 20 min)...is this doable?

then the next day from Kanazawa to Kyoto by taking JR Thunder Bird #36. My worry is spending extra time & cost to Kanazawa...are these Kenrokuen Garden & Kanazawa Castle worth seeing. Anyone been there done it?

Both the busses you've mentioned require reservation; the latter bus is operated by Hokuriku Railroad.
If you can hold a Japan Rail Pass, the Pass covers fares and charges between Takayama and Kyoto / Takayama and Kanazawa / Kanazawa and Kyoto.
http://www.japanrailpass.net/eng/en002.html

I suppose it can be a hectic trip to come into and go out Shirakawa-go in 3 hours or so; it's better if you can reach Shirakawa-go earlier or lodge there.
- Shirakawa Village: Tourist info
http://www.shirakawa-go.org/english/index.html
- japan-guide.com: Shirakawa-go and Gokayama
http://www.japan-guide.com/e/e5950.html

To visit Kanazawa, I guess your plan will do. Thunderbird #36 leaves from Kanazawa at 16:03 ; maybe it' better to stay there longer.
- Kanazawa City Tourism Association
http://www.kanazawa-tourism.com/
- japan-guide.com: Kenrokuen Garden
http://www.japan-guide.com/e/e4200.html
- japan-guide.com: Kanazawa Castle
http://www.japan-guide.com/e/e4202.html

When you lodge in Shirakawa-go and skip Kanazawa....
Takayama 12:50 ;
| Nohi Bus (requiring reservation) #;
around 13:45 Shirakawa-go: tour and lodge;
Shirakawa-go 06:53 ;
| Nohi Bus (not requiring reservation) #;
around 08:00 Takayama 09:37 ;
| Ltd. Express (WideView) Hida #6;
12:01 Nagoya 12:22 ;
| Shinkansen HIKARI #509;
13:15 Kyoto.
# The round-trip bus fare is 4,300 yen per adult.

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Is there a train or highway bus that goes into Kyoto city from Takayama (not drop off from the highway)?

The bus from Takayama stops only along the expressway and does not enter central Kyoto.

By train, you can conveniently travel from Takayama to Kyoto with one transfer along the way in Nagoya.

This is helpful...I have difficulty to call NohiBusReservation Centre because on the web site it indicates "Japanese only" which I don't speak. Do you know if they have a fax no?
OR
Do you think seats will be still available if I book it on Sept 30 for Oct 2 tickets because I will be arriving Takayama via Tokyo overnight bus to Okuhida Hot Spring Village, so I thought I will reserve the seats that morning.