90 days trip

Hello,

In a previous question you informed that it was fine to buy three 21-day passes to use during my 90 days trip to Japan and activate each of them as the trip progressed, provided that I observe the three months exchange limit. I have a couple of follow up questions:
1- By "exchange limit of 3 months" you mean the date of exchange of the voucher I will get in the USA for the actual pass in Japan, correct? I ask because the date of validity of the pass itself could be longer than the 3 months after the voucher issuance.
2- Can I exchange the voucher for the pass at any JR station in Japan?
3 - Does JR have an online tool or app that analyzes an itinerary of cities and dates and proposes an optimized train / bus schedule?
Thanks.