We were looking for a combined pas for the following itinerary - Shinjuku - Kawaguchiko - Matsumo...

Hi there,

There are some passes I can remind of and hopefully recommended to you.

Kawaguchiko area;
https://www.fujiq.jp/en/qpack/
Q pak covers your transportation from Shinjuku to kawaguchiko and the fee for Fuji Q Highland is included.
*also includes one way bus fee for back to Shinjuku
http://www.odakyu.jp/english/deels/freepass/fujihakone/
This pass will cover not only Fuji Kawaguchiko area but also Hakone.
You can find the details from the link above.

Matsumoto - Shirakawago area;
http://welcome.city.matsumoto.nagano.jp/modules/xpressme/events/2-days-free-bus-passport-4-days-also-available
This pass is quite useful to tour all around included area.
Valid is 2 days and 4 days.

And as you plan to, Kawazawa to Kyoto would be better by train.

And also there are pass from JR;
http://www.japanrailpass.net/en/index.html
Please see more details from the link above and check it out if it will be useful for you.

Hope this can be your help!