If we buy a japan-rail-pass from this site, will we get an actual pass or a voucher?
Since I am guessing it will be a voucher that needs to be exchanged, what is the best (=fastest) strategy to exchange the voucher for the actual pass? Can it be done _before_ customs, or do we need to stand in line for an hour or so (Kyoto took us 2 (!!!) hours) before it is our turn to exchange?
Since you are outside of Japan, it will be a voucher. The busy stations and airports can have lines from 30-60 minutes, or even longer. But there are many stations you can exchange the voucher for the pass. See here:
If you choose a smaller station or other place early in the morning, you can avoid a lot of the crowds. You do not have to exchange the pass on the day you start to use it - you can designate a future date as your first day.