As far as Q1 is concerned, I am not sure where in Tokyo you would pick up the ticket from Shinjuku to Takayama. There are several "highway bus" websites for Japan. If it was this website,
http://highway-buses.jp/takayama/... then I would call the phone number on the website. If you ordered online, they must have sent an email outlining the details?
Q2 is a bit more complicated. I've not heard of the pass you name. I got this pass,
http://www.alpico.co.jp/access/ticket/006.htmlfor four days of unlimited travel within the Okuhida area, including Shin-Hotaka, Hirayu, Kamikochi, Takayama, and Matsumoto. It wasn't a huge discount, but I did save some yen (a few hundred) and it was very convenient, instead of paying bus fare with each trip.
Are you planning to go to Kamikochi? (it is worth it, in my opinion, especially since you're so close!)
Are you planning to return to Tokyo via Matsumoto and Nagano, rather than going back via Takayama?
Y12,000 is pretty steep, but can be worth it, if you're planning the Ropeway, and Kamikochi, and other travel. But, if you are just going Takayama to Hirayu, then Hirayu to Fukuji, and omitting Kamikochi, then it isn't worth it.
The two day Takayama-Hirayu-Shinhotaka pass won't work for you either, since your travel takes place over more than two days.
You'll have to check the prices of the individual trips online
takayama to shinhotaka onsen, about Y2160
shinhotaka onsen to hiraru onsen, about Y700
hiraru onsen to kamikochi about Y1160
kamikochi to matsumoto about Y2450
Sorry for my late reply, I see you're traveling soon! I am currently on vacation, so haven't been checking this forum. Good luck!
Dale