How to plan the route for my travel?

Dear Friend,
I wish to cover these places in the 1st 2 weeks of May 2018: tateyama kurobeAlpine route, kamikochi, Noriku Kogen, kiso valley , Ainokura farm stay. I am travelling by train. I am flying from Singapore.
1)Should i fly to Tokyo or Nagoya to start my trip?
2)What should be the order of my tour?
3)Which train pass should i get?
Thank You for your advice

Kamikochi, NorikuRA Kogen, Ainokura farm stay are not accessible by train, you need a bus to reach them. I'm guessing the farm stay has a bus or shuttle option that you have researched.

Alpine route and kiso valley you'll need a train option.

The route you take will depend on where you fly in and out of. Make some decisions first so others can help you further.

Kamikochi and Norikura Kogen use the bus system between Matsumoto and Takayama. Alpine route usings systems between Toyama and Shinano Omachi / Nagano. And your farm stay look close to Shirakawago, so either Takayama or Toyama access.

Looking at the places you wanna go. It looks like you'll need to do a big Z across Chubu, so either Nagoya or Tokyo will work. So pick whichever works best or interests you more. Trains from Nagoya should be cheaper as you wont need to use Shinkansens to move around.

Please note that the first week of May is "Golden Week" in Japan and thus VERY crowded no matter where you go. All the places you've mentioned are quite popular, so also keep that in mind.