The simple picture of this era one gets is that of a homogeneous, unchanging country, with broadly delineated lifestyles as one goes further from the capital or down the social scale (I imagine this image is has been created by orientalists, Japanese nationalists, and storytellers, rather than strictly from history). I am going to give four examples of a simple statement one hears (regarding political, international, ethnic, and religious practices), and then the tensions I imagine contained within it. I am looking for histories which look at how these features worked in practice, especially in non-elite contexts:
(1) There is a claim (for example: wikipedia) that samurai were the "ruling class". Yet there was no electoral representation of samurai; the idea being that they had cultural prestige and social (+ political and/or legal?) rights sufficient to broadly let them be in the driver seat. Given that Edo was an era largely of peace (thus further weakening samurai bargaining power), I would expect the social, economic, and political strength of samurai to decrease unless there was institutional counterweights. How did they experience their era of "ruling"? Was there a polarization between samurai who found non-military sources of power and those who did not? In what sense did the official hierarchy resemble reality?
(2) There is an idea that Japan was effectively sealed from the outside world due to central government policy. How effective was this Sakoku? It's hard to imagine such a restrictive policy being possible on such a large scale using pre-modern communication and state capacity--was it negotiable at the peripheries of the country? Were small time traders able to buy off local leaders who then reported back nothing to the center?
(3) There is a nasty 20th century idea that Japan is and has been one of the most "homogeneous" countries racially in the world. I know from the European example that modern states can create perceptions of ethnic homogeneity where there wasn't such before, and I assume this happened in Japan because even as late as "in prewar Japan, everyone said that Yamato people are hybrid people (zasshu minzoku), and mixed people (kongo minzoku)" [quote from Kamishima Jiro, and found in John Lie's Multiethnic Japan]. Thus in the Edo period, I would assume that there was diversity of language, custom, identity, and perhaps even "ethnicity" (or something similar) within what is now considered simply "Japan".
(4) In the 20th century, "[Shinto] shrines across the country were being merged, as local gods were dragooned into the service of a national system of State Shinto, focused on the Emperor and his imperial line" (Christopher Harding, Japan Story). I assume this created an official version of Shinto which often overrode local traditions and homogenized practices.
Tl;dr: I am interested in a history of Edo Japan which deals with the fact that political castes have to be actively maintained, that it must have been very hard to enforce sweeping top-down policies, and that ethnicity and religion are not fixed at the grass-roots level. In short, I am interested in a history of the period that sees Japan as a large and diverse place, not one simply reflecting the imperial court and high politics (as interesting as that can be).
Any recommendations? :)
My top recommendation to cover what you're talking about is Stranger in the Shogun's City: A Japanese Woman and Her World by Amy Stanley. You may also like the period account Lust, Commerce, and Corruption: An Account of What I Have Seen and Heard, by an Edo Samurai
That being said, there are a number of structural issues you're raising which are not the focus of those "grassroots view" books. I'm going to do my best to tackle these.
(1) Yes, the samurai were becoming increasingly impoverished as the centuries went on. They were paid from the central treasury but were paid on the rice standard, which depreciated considerably over the centuries. Lust, Commerce, and Corruption describes this in detail.
(2) During the sakoku period, trade with Korea, China, Ainu Mosir, and the Ryukyus continued. It was farther afield, places like Vietnam, Brunei and Europe where Japanese were banned to go. Raising capital for an expedition to one of these places would have required significant expenditure, and I think it simply would have been too risky and not profitable enough to attempt to smuggle goods to Vietnam. There was enough smuggling going on to and from China, as mentioned by David R. Ambaras in Japan's Imperial Underworlds.
(3) Your intuition is correct and there were certainly a variety of dialects and self-identities in Edo period Japan. People identified as subjects of their own domain (literally country, kuni/koku) first, and as denizens of the archipelago second. Eiji Oguma writes about this in A Genealogy of "Japanese" Self-Images, although that book is almost entirely about the Meiji period, not Edo. (I know there are other Edo period experts on this sub and I hope someone can help me with this.)
(4) This is kinda true, kinda not. The goal was to create a new, totalizing version of Shinto and this was kind of accomplished in the 1870s, and kind of during World War II, but also kind of never completed, and there is still a lot of diversity within the newly created category of Shinto. I don't know what you would like to read that might reflect the pre-1868 situation as before "Shinto" there was basically everything: shrines, folklore, urban myths, yōkai. One history-focused publication is A New History of Shinto by Breen and Teeuwen although they couldn't quite succeed at the massive undertaking they aimed for. I can recommend other books as well depending on your interest.