Is everyone more there to see friends than local sights? If there are actually things people really want to see/do, I'd ask for a stack ranked list. Those who are already near Japan time zone might be on a more normal sleep schedule or able to do late nights while those coming in from US will be awake in early morning. There's a difference in activities: early morning - shrines and outdoor parks. Late night (aka after 8-10 pm) - Izakaya, bars, karaoke (most indoor attractions close by 8 pm if not earlier except for a few offering night views and remaining holiday illuminations/markets).

Japan-guide is a good general tourism guide for first time tourists https://www.japan-guide.com/ though you may get a wishlist of things like "weird anime stuff" (Akihabara), "Kill Bill restaurant" (Gonpachi), or some other pop culture. Good news is that all of it is new to you and presumably them, so you have more things people want to do together and can prioritize your shared interests list rather than a "First Time Visitor" checklist. Book any reservations ASAP since it is quite soon & peak travel period, especially shinkansen trains and if someone wants specific higher end dining.

New Year's is usually a family holiday in Japan. People tend to get up quite early on Jan 1 to go to shrines/temple with family so any shrine heavy area will be crowded (such as Kyoto). Kyoto is usually very crowded from over tourism so adding in domestic travelers and people returning home for the holiday means booking shinkansen train tickets ASAP, especially if you want to sit with your travel group. All JR bullet trains Nozomi (fastest train) between Kyoto, Shin-Osaka, and Tokyo are reserved seats only during that time. Major museums and stores may be closed.
The Hiroshima Peace Park Museum is closed Dec 30-31 https://hpmmuseum.jp/?lang=eng There are reserved hours on open days which I'd aim for to minimize crowds. I believe the outdoor section should be accessible Dec 30-31, but you should double check.
*ETA Peace Park Museum is actually open on Jan 1 according to the advance online tickets.

1. Which airport are you landing at? KIX? TYO? If you need to get to Osaka region from an airport, I'd book actually book a flight if you can bundle it into the same ticket because of the peak travel period. Saturday evening train tickets could be sold out if you try to purchase on arrival. The domestic airport is ITM as an alternate to KIX. https://www.japan-guide.com/e/e2433.html
9. I'd leave off a stopover at Fuji and onsen. Once again, peak domestic travel period. Booking an ryokan onsen at this time, especially if solo, is going to be very slim pickings and at very premium prices.