It appears that you'll be in Japan for 10 nights? If so, presumably you'll get a 7 day JR Pass .... in which case you need to activate it so that it covers days 4 -10 (or it'll expire before you get back to Tokyo) .....
Now that I re-read your original post, I'm somewhat unclear how many days/nights you are in Japan? You just need to make sure the 7 day period for the pass covers your trip from Tokyo to Toyama and to Kyoto and then back to Tokyo/Narita again before you fly out.
You can
exchange the JR Pass voucher for the actual pass at any time (so do that in Tokyo as soon as convenient). When you do so, you have to tell them what day you want the Pass to actually start, so make sure to pick the right date, to get the maximum value out of the 7 days.