Splitting this out into its own post but I had the fortune of visiting a few awesome coffee places this time. And now it turns into rambling. 
Apollons Gold - Akasaka store
I heard this is a great roaster online and they had a new store/roaster in Akasaka so decided to visit. The location is fairly convenient and the space is really nice (though I’ve been to ones that are better for enjoying coffee - actual tables vs fancy benches). There was surprisingly no line, but maybe it was the weather. I had an awesome pour over and immediately bought some coffee beans, though they had to dig in the back for that specific one. Would recommend.
Fuglen - Shibuya store
I’d previously done the three drink coffee tasting at the Sangubashi store (similar to the Glitch flight but more focused/less options with some fuglen specific twists) and was quite impressed. Didn’t have time for a full tasting this trip but did have some time to drop by the Shibuya store.
This store is interesting in that it opens rather late and transforms into a cocktail bar. I, however, grabbed an iced coffee and a pour over. The iced coffee was great. If you get a drink and sit in, you can order another drink without getting back in to the sometimes long line (or at least I was fine at the counter). Unfortunately, for pour over, they only offered aeropress at the time. A solid drink but I kind wish I could taste the actual pour over version. They have other locations and I’d probably consider them next time if I have time. It’s still a cool store to visit but I’d try other drinks if the aeropress is the only option for pour over. Or maybe I should try a different bean.
Onibus - Yakumo location
I’d previously gone to Onibus Nakameguro and came away thinking I missed something. Saw somebody on reddit mention having a great Rwanda and I was a modest walking distance from this location (I didn’t know they had so many) so decided to give the chain a second shot.
The shop is a little off the regular Tokyo track. But it was a very nice shop in a rather well to do residential area. They had a Rwanda and that’s what I got. A great pour over and the chain is back on my list after this cup.
Cokuun - Omotesando (location revealed only after booking)
I heard about this from Jack at endorffeine and had to give it a shot. It’s run/owned by some barista coffee champion types. Rather pricey for a coffee omakase, but I can see why as it’s a whole nother level of complexity. It’s pretty eye opening in many ways. The tastings are very small group (less seats than Hayato) and they approach coffee and coffee beans in a very different way from my experience. Over half the seating were a group including coffee professionals from China (specifically Shanghai - seemingly a Chinese megahub for coffee) where apparently coffee has gotten very serious very fast. Just listening to their discussion was super interesting. I was clearly the least serious of those there, but still very warmly welcomed. It was well worth it in my opinion but I think coming in with an open mind will be quite helpful. It’s unique enough an experience I’d prefer not to spoil more but I’m sure there’s plenty more nuanced discussions elsewhere online. Oh also it’s a beautiful space.
Leaves Coffee Roasters - Asakusa/Sumida
This is clearly a famous coffee roaster. My first experience with this roaster was at a Koffee Mameya Kakeru tasting but I’d otherwise have known from the line of foreign customers and the almost monk-like appearance and attitude of the main brewer. As another sign of Chinas coffee scene, I spoke with another coffee professional with a shop in ningbo standing next to me in line.
Anyways, I got there at roughly 3 PM and waited 30-40 minutes to order. And this was partially thanks to the couple in front of me bailing right before being seated for some reason. Though after 4 pm the seating does open up (shop closes at 5 though). I had 2 pour overs, both of which were absolutely delicious. They also have some pretty cool looking serving option involving milk, espresso, a thermometer, and evaluation of temperature changes. The brewer himself seems to use a more complex pour over recipe but I don’t think my understanding is good enough to properly relate what he said. Additional drinks do not require waiting in line. Nor does buying coffee beans. You just wait the line once and ask the staff if you have additional orders. The space itself is also pretty nice and well suited to enjoying coffee so long as you can ignore anybody anxiously waiting for a seat.
Honorable mention:
Camelback - Shibuya
Met a fellow frequent Tokyo traveler from Australia who showed me this coffee shop. A bit more of a coffee stand with food. Hidden away in the backstreets of shibuya. Had a nice iced americano. I’d consider it again were I to be in the area.