My questions:
1) Possible to do Kiso Valley from Nagoya in a day?
2) I am a JR pass holder, many said that Shinano limited express does not stop at Nagiso. Correct?
3)Alternative, will it be better if go and return via Nakatsugawa only? It mean i will trek from Magoma to Tsumago and take bus back from Tsumago to Magome.
4) Is the JR pass cover the bus ride from Nakatsugawa?
5) What is the best way to check whether the bus ride cover by JR pass or not? Or any website of JR bus ride will help?

Yes, it is possible.

I am a JR pass holder, many said that Shinano limited express does not stop at Nagiso. Correct?

Most don't. A few do. Here are lists of those that do:
http://grace.hyperdia.com/cgi-english/hyperWeb.cgi?H_CM...
http://grace.hyperdia.com/cgi-english/hyperWeb.cgi?H_CM...

Alternative, will it be better if go and return via Nakatsugawa only? It mean i will trek from Magoma to Tsumago and take bus back from Tsumago to Magome.

No, the round trip options is better.

Is the JR pass cover the bus ride from Nakatsugawa?

BTW, UJI:

I like the "table form" of the train time table that you give me, that show train no & time to different station from my chosen departure and destination. (previous reply under the same thread) However, whenever i access Hypedia,i can only reach to the page as below:

http://grace.hyperdia.com/cgi-english/hyperWeb.cgi#TOP

1)Can you please advise me how to go to the summary page that present in a "table form" showing all the different train no and time, passing through different station before reaching the chosen destination? It helps a lot. Please forgive my long description. Hope you can understand what i mean.