1) I saw some information and I think I should buy the second pass here right?
http://www.tobu-bus.com/pc/ticket/nikko.htmlYes, that is right.
I found the bus timetables here but having problems with the Japanese
http://www.tobu-bus.com/pc/area/pdf/2009_nikko0725.pdf
Note that this is the summer timetable (valid until November 30, 2009).
i) For Toshogu Shrine area, should I alight at 西参道発?
I personally suggest to alight at 神橋, the sacred bridge. Then, you can see the bridge and it is not too far from there to the shrines and temples.
For Lake Chuzenji, I'm not sure what is the difference between 中禅寺温泉着 and 中禅寺温泉発.
着 means arrival
発 means departure
iii) Does it mean I can take the 世界遺産めぐり bus to 大猷院二荒山神社前発 for Toshogu Shrine area too?
Yes, this is the bus that takes you the closest to the shrines and temples. For Toshogu Shrine, I recommend to get off at 表参道.