Hi!
If you're coming through in November you MUST start in Ogizawa if you hope to make it to Murodo. Please see here:
https://www.alpen-route.com/en/about/seasonal.htmlIt is possible because of snow that the whole route is not open, so staying overnight might not be an option.
If you are going: Narita to Shinano-Omachi; Shinano-Omachi to Kyoto (which is likely to be by way of Nagoya); Kyoto and Osaka and then Osaka to Hakone; Hakone to Tokyo; Tokyo to Narita a pass might not be worth it. I am assuming on all trips with seat reservations you want a seat reservation
Though you save some money getting a Narita to Shinano-Omachi ticket, it might be worthwhile to get the JR East NEX special since you will save I believe more money on your return. Using current times the earliest you are going to reach Shinano-Omachi is 14:15 (figure 1 hour from your 7:30 am arrival time to get you on your way from Narita.) The train fare is: 10,370 yen from Tokyo (plus the 4000 yen JR East Special to ver the roundtrip NEX)
Whatever part of the Alpine Route you can do is not covered by a JR Pass.
Shinano-Omachi to Kyoto is 10,300 (assuming you can't complete the route)
Toyama to Kyoto is 8950 yen (assuming you can complete the route)
Kyoto to Osaka is negligible at around 560 yen one way. You're unlikely to take a shinkansen because they are not all that frequent and you would need to change in Shin-Osaka anyway.
Without a rail pass it is 12,730 yen to Hakone-Yumoto from Osaka, however 310 yen of that is a private line not covered by a pass.
From Hakone you can get back to Tokyo either by shinkansen or private line should you not have a pass. It's 3850 yen (again inclusive of the 310 private line not covered) if you were to take a shinkansen though again you can get there cheaper on Odakyu.
So I'm getting a total of: 41250 or so yen, If you go through Toyama it is cheaper. So it's about 50-50 whether a pass is worth it. Passes are great, but they do restrict you from using nozomi which are a LOT more frequent.
I hope this helps!