Jl17. Out of past 62 flights, avg delay is 8 min, max delay is 21min. Only 2 have delays above 15 min

Basically, this is doable. Only risk = crowds @ customs/JL pass office, and they are small risks given the amount of buffer time you have

figure out a backup plan if you get delayed. As I said, you can still make it to Tokyo (or as far as Nagoya) and pay out of pocket for a cheap hotel room there.

Keep track of the time, and go to backup plan if you're still waiting on Jr pass line 5 minutes before last NEx departure for shinagawa/kyoto

That was what I was doing for my trip