Help with travelling across Japan

I have put together our itinery for travel to japan in may of 2020. I would greatly appreciate any help and comments as to improvements. where would be a good place to start our 21 day japan rail pass. we could also get a shorter regional pass to complinent our japan pass. can you suggest a better base anywhere to see these sites. we will fly from Canada to Sapporo first to visit a friend in ashoro. then to Okinawa so that we might miss the start of rainy season. my itinerary is as follows: Sapporo- 3 nights, ashoro-2 nights,otaru-2 nights, fly to naha-7 nights, fly to Nagasaki-3 nights, fukuoka 3 nights, matsue 3 nights, Hiroshima/miyajima 3 nights,matsuyama 2 nights, kochi 2 nights, beppu 1 night,takamatsu 1 night, Kyoto 9 nights, Tokyo 8 nights, I would like to shorten my stay to 40-45 days and if my stays are too long I can shorten them. also I could return home from another city other than Tokyo. thanks to any comments or input for our itinerary.

Otaru is probably best as a day trip from Sapporo and catch the train back at night. Without a car, you will be limited to what you see there (around Otaru)

I dont think any JR nationwide passes are viable options. You really only need it for Nagasaki to Tokyo. And you take longer than 7 or 14 days to do that. The the 21 day pass would cost more than you long distance train travels.

Most rail passes, larger regional ones included, they don't suit extended travel plans like yours. As they limits of days are too short. You need to look at the smaller city type passes, and just pay for your long distance travels as you go. Buses, ferries, trains etc.

Hmmm I don't know, I think if OP moved some destinations around, OP might be able to make one of the JR West passes pay off. It's late and I'm exhausted but the itinerary if it really is as written does jump a lot. Beppu to Takamatsu is a 5-6 hour trip.