This is my family (husband and teen son) first trip to Japan coming from the US. Please see if this itinerary and number of days in each location make sense, or if some of the days should be relocated elsewhere. Also there is the possibility that I can add 2 more days to this itinerary. If so, should I add it to one of the already chosen locations or a new one like somewhere in the Alps? Here it is:
June 2-8 (6 nights) in Tokyo with one or two possible day trips?
June 8-9 (1 night) in Hakone
June 9-15 (6 nights) in Kyoto with day trip to Osaka and elsewhere?
June 15-17 (2 nights) in Hiroshima/Miyajima
June 17-25 (8 nights) in Hokkaido, locations TBD
Thanks!

Your basic itinerary looks good to me, but it's hard to say for sure since you haven't told us about your interests or aspirations for this trip.

I tend to think it's best to plan 5 or 6 nights for the combination of Takayama (in the Alps) and Kanazawa (immediately adjacent); YMMV.

If you want something mountainous (but not Alpine), Nikko might be worth considering. Or Koyasan. Or add time to Tokyo or Kyoto based on your interests.

Have you consulted japan-guide.com?

It does look good, so far, but we can help more if you told us about your interest, as kja mentioned.

You could fly nonstop from Hiroshima to Sapporo. You could add a night to Hiroshima. Or two nights in Fukuoka and fly nonstop to Sapporo from tnere. Am fairly sure that other Hokkaido airports would require a connection (no big deal and probably Tokyo Haneda).

If interested in hot springs, then Noboribetsu Onsen should be on the Hokkaido plan.