It definitely sounds like you got around a lot during 'only' a 6 week stay, that's awesome!
Oh man, I miss that part of Kyoto, so much stuff crammed into such a tiny street. Not completely crammed in like Golden Gai in Shinjuku; as a foreigner, it felt a lot more welcoming and chill.
Shinjuku and Golden Gai are still some of my favorite areas in Tokyo, busier, dirtier and seeder than most of the rest, it felt more real.
Most business travelers there end up around Tokyo station. My suggestions now are to go out to Shibua/Shinjuku area, that area is more like what I imagined Tokyo to be like. The no foreigners signs on some doors in Golden Gai did feel strange. I did the good old おすすめは (what's your recommendation) in a bar in Golden Gai and we settled on a gin for his home town up in Sapporo.
I liked it so much that on our trip to Hokkaido, while we were in Sapporo, we went out to the distillery. I got 4 different bottles and brought them back here.
https://goo.gl/maps/FqdRN8UoAuFPmZzo8
That said, I had similar experiences with some of the smaller stops I madei; I stayed in Noboribetsu in Hokkaido for a night, and despite it being a somewhat touristy "onsen town", the tourists they're expecting are Japanese travelers who aren't looking for many amenities outside their ryokan.
Yeah, the areas that are thick with nice ryokans sometimes don't have much outside of them, the are basically all inclusive. We ferried out to Sado and stayed in an amazing one there.
But venturing around the island during the day it was not easy to even find open restaurants.
Similarly, a day trip I made out of Sendai to Yamadera (amazing view once you've climbed to the top, maybe not so much fun climbing up), even with Tendo being right there, it seemed like the moment you left greater Sendai you were... very far from urban comfort. I loved it, but not so great if you just want a modern coffee shop with all the amenities to relax in for a little while.
With Senda only being about an hour north by train from Utsunomiya and the access it gives to a few other amazing palces, it's one of my new top recommendations to people for a weekend trip. This would even work from Tokyo, it's only 1.5 hours by train due to the Hayabusa connecting the two.
Friday - Grab ekiben, beer/wine/sake, get on train, go to Sendai. Check into hotel, drop off bags, go out to second dinner and/or bars.
Saturday day - Go out to Matsushima. Make sure to go to
Godaido of Zuiganji Temple,
Fukurajima Island,
and especially the walk back to Zuiganji Temple
Saturday Night - Dinner and drinks around Sendai again. If interested in trying Sake I highly suggest going to Hatago,
https://g.page/hatago?share
It was one of my favorite dinner and sake experiences in Japan.
Sunday - Check out, Most stations have lockers, so leave your bags in Sendai station if coming back through, or in the station you will go to. Head over to Yamadera to take the one thousand steps hike up to Risshaku Temple, the one you were talking about. This is one of my favorite combinations of history, culture, nature and hiking that we did our entire time in Japan. There are dozens of temples to stop at one the way up. Yes, it's definitely off the beaten path, but at least the train to there takes IC card.
Thanks for the walk down memory lane, hopefully it sparked some more memories for you too.