Hi again!
1.) It is possible to book all your tickets at the moment when you activate your JR Pass. Please bring a printed list with the dates and routes you wish to travel on, this will make the process to lot quicker and the JR Staff will be thankful as well!
2.) Yes you can ride the Bullet train to Odawara station with the JR Pass and buy a 3900yen Hakone pass at Odawara station.
3.) I am not aware of a sightseeing bus service, however there could be one. You could also consider using a Taxi to travel around Kyoto, prices are not too high, especially when you split it among your travel party. I would recommend traveling as early as possible to make the most of your day in Kyoto.
4.) The same applies for Atami, you can use the Shinkansen and JR Pass to travel there.
5.) You can use the JR Pass for local travel around Tokyo as well. I would recommend a visit to Tokyo station, Harajuku, Shinjuku, Omotesando, Shinbuya, Ginza, Ueno and Asakusa.
6.) You will have to pay all fees related to the Ski resort. Including entrance and rental fees.
7.) It looks like a good plan and you would be making great use of the JR Pass. However I would consider spending a night or two in Kyoto as the city has a lot to offer.
Currently shipping to India takes 4 working days which should be more than enough to get the pass to you. You can find all the details HERE.
Lastly the JR Pass can also be used for travel to Yurakucho and you can walk from there to the conference center.
Hope this helps!
Daniel