Itinery advice - alpine route

Please advise if this itinery makes sense or if there is a better option
Day 1 - depart Tokyo for Matsumoto and over night
day 2 - Do Alpine route from Matsumoto to Tpyama and on to Takeyama to arrive in Takayama by 530 pm (is this doable?).overnight Takayama
Day 3 - explore around Tkayama and overnight
Day 4 - on to Kyoto or Osaka - which is closer?

Does this make sense? Any other suggestion? Will Japan Rail Pass work for all steps?

day 2 - Do Alpine route from Matsumoto to Tpyama and on to Takeyama to arrive in Takayama by 530 pm (is this doable?).overnight Takayama

If you start early and travel at a fast pace, it should be possible.

Here are train timetables:
http://www.hyperdia.com/

And here are last year's timetables for the Alpine Route (likely to be similar to this year's timetables):
http://www.alpen-route.com/en/transportation/timetable-fares

Day 4 - on to Kyoto or Osaka - which is closer?

Kyoto is a little bit closer as seen on the following map:
https://goo.gl/maps/BMi67

Does this make sense?

It sounds good to me.

Will Japan Rail Pass work for all steps?

Certainly not. The Alpine Route is not covered by the pass!

I would stay overnight Toyama on day 2.