Just a few thoughts:

I honestly can't imagine spending 3 nights in Narita town even on a longer trip like yours. But if they are still in print, get copies of "Day Hikes near Tokyo" and "more Day Hikes near Tokyo." One of them has a decent day hike around Narita. Also there is the National History museum not far from Narita on the Keisei line. It has a good English headset tour.

I've done the night in Miyajima. If you've been during the day already, I don't think it's worth returning. Also unless things have changed recently, the hotel rooms are hugely dated and well overpriced for what you get. Also pricey is the only restaurant on premisses open for dinner.

No Hokkaido? Should be manageable in May. You're missing 1/3 of Japan if you've never been. But distances are longer than elsewhere and lots of it is best seen by rental car. Should be even easier for you, you come from a place that drives on the left! Sapporo is definitely not among the most interesting places to visit in Hokkaido. Unfortunately, those are in Northern Hokkaido, national parks and such. You can get there fastest by flying to Memanbetsu and renting a car at the airport.

One night at Himeji is plenty to explore the castle and environs. For me, even too much. Better yet, an easy day trip on the way to or during your stay in Hiroshima. Japanese castles in general are far better to look at from the outside than to visit.

For me, 5 nights in Osaka would be 4 nights too many. Have you thought of trying to stay at a ryokan or two in the vicinity instead?

When in Nagasaki, I thought it worthwhile to take the boat excursion to Gunkanjima, the "battleship island." They say they are going to land but when I went they came up with an excuse not to. Still worth it to circle the place close up. There also is a Gunkanjima museum that might be worth visiting before the excursion to get some context in advance.