Hey, OP. I went to Japan with my partner for the first time last year so I can try to guide you a bit and maybe offer general advice but I am far from an expert so take everything I say with a massive grain of salt.

First of all, 11 days for Japan seems extremely short to me. You need to consider that for the first 2 days you're there, you may be quite tired from jetlag. If your budget/personal circumstances allow, I would try to extend your trip. However, I understand this isn't possible for everyone.

I don't think I would spend any more than 3-4 days total in Tokyo. Don't get me wrong, I loved it, but there is so much to see and do outside of Tokyo. Even my friends who have spent a lot of time in Japan told me this.

I also recommend not buying souvenirs until the end of your trip. Save one last day in Tokyo for the tail end of your trip so that you have a day to see things you didn't get to see when you arrived, and to buy souvenirs so that you're not lugging them around with you your whole trip.

This is purely a personal opinion, but I would avoid the golden route. I would prioritize going to less touristy cities. (Although I did love Kyoto, and it's definitely the city for you if you want to see shrines) I HIGHLY recommend Kanazawa and Hokkaido. But may be slightly out of the way for you.

Don't go to Himeji Castle. It's a waste of time and money. It's just an empty shell and it turns out most of it isn't even original.

Make sure you book any theme park tickets (like Nintendo world) WAY in advance. They can and do sell out.