I am returning to Japan for my second time and will be there from 11/16/18 - 12/2/18. My stops are as planned.
11/16/18 - Arrive in Nagoya. Will use subway to hotel.
11/17/18 - Explore Nagoya area.
11/18-24/18 - Travel and stay in Kyoto. Spend the week seeing local area sites. Day trips to Osaka, Nara and Kobe.
11/24-1/18 - Travel and stay in Tokyo. Spend the week seeing local area sites. Day trip to Mt. Fuji.
12/1/18 Travel back to Nagoya for flight home on 12/2/18.
Which pass will be the best value. I was thinking 14 day pass and activate it on the 18th when leaving for Kyoto.
If you purchased a 14-day JR Pass, it would actually cost more than what you'd spend paying the normal fare for each trip within any 14 days in your stated itinerary.
You are looking at 40 thousand yen at the very least.