What did the Japanese military do to maintain their fighting edge during the Edo era/Bakufu (1603-1868)?

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It is a misunderstanding to talk of an unified Japan during the Tokugawa period with respect to having its own army, etc. These notions only become relevant after the concept of the "nation of Japan" was created in the 1860's and 1870's.

In effect, every han or domain was its separate state though they paid homage to the Tokugawa overlords. These han can be divided into closely linked (shinpan and fudai) with the Tokugawa (e.g., Aizu and Tsuruga) and outsiders (e.g., Satsuma). In effect, this means that we are dealing with the militaries of scores of different 'states' as the internal politics of each han was left to the individual ruler, with the shogun responsible for foreign affairs, commerce, and national security but the daimyō administered their lands independently.1

However, in most cases, Tokugawa policies prevented the daimyō from aspiring too far. One of the most notable aspects of this was the alternate year system or sankin-kotai—a major drain on the domainal economies. In fact, it was only after sankin-kotai was discontinued in 1862 when many domains started to modernize their armies and buy foreign ships (though several had done so already previously). Other significant policies were the ikkoku ichijyō rei and buke shohatto which both laid down obligations to the han and also prevented them from building castles without shogunal approval.

Meanwhile, waging war was made more difficult by centralizing the action to the new government and restricting the possession of arms. Warrior monks had been defeated in combat and peasants had been demilitarized by Oda Nobunaga and Toyotomi Hideyoshi, but Tokugawa Ieyasu expanded this to allow samurai to give up their status and become peasants while others gave up their land for a yearly retainership.

Therefore, there was no official shogunal plan for maintaining military education or training troops for war excepting some very small, bodyguard-like, units that were in constant readiness.

Shogunal Military

The shogun did have a special group of samurai, the hatamoto, who were his direct retainers. These had served as guards during the preceding sengoku jidai, but in the Tokugawa period they essentially became the Shogunate's army with every hatamoto expected to serve militarily when called upon (though many primarily filled administrative roles).

...by 1635, the earliest date for which reliable figures are available, their number stood at about 5,000 men. Because of their obligation to supply troops for the shogun in addition to their own personal service, a call to arms of the hatamoto would have resulted in an army of about 80,000 men. This figure included those who occupied the third tier of the hierarchy, below the hatamoto, who were called yoriki or gokenin; these commanded the 'line infantry' squads of dash in or ashigaru footsoldiers within the Tokugawa army.
—Turnbull, 'Hatamoto'

However, as inter-han warfare had ceased, the hatamoto gradually lost military significance while turning more and more into policemen. Many hatamoto also served as martial arts instructors.

There were also a limited number of horse guards' units. The most formidable of these were the Great Guard of twelve companies (after 1632) of 55 men each. The Goshoinban were similarly organized with a more specific role of guarding Edo Castle. In addition, after 1643 the Goshinban of eight companies (by 1724) of 60 men each was created for further security in Edo Castle but also protecting the shogun.

Samurai Education

As all samurai, incl. the above-mentioned hatamoto, were expected to be able to be called to arms if the need arose, it also bears to consider their education. This is a difficult subject to find good overviews on, and my own reading focuses on the mid-19th century so this might be different in the early period.

Overall, in the mid-19th century, the focus was on administrative subjects, incl. writing, calligraphy, classical Chinese (both poetry and literary classics), and a uniquely Japanese subject called national studies. At the same time, however, most young people would have been expected to study swordsmanship, both as an avenue into philosophy and to improve their martial skill. Spear schools also existed, with some of the leading Meiji reformers having studied that (though I'm not sure if that was instead of the sword or alongside it).

I believe that horsemanship was in decline, at least amongst the lower samurai ranks, though the nobility probably learned this skill—if anyone can support this either way, that would be appreciated. Cavalry did not form a significant part of the Bakumatsu-era armies, however.

The philosophy that the samurai studied is represented both by Nitobe Inazō's 'Bushido' as well as historical writings and events which represented the ideal warrior's code, such as 'Hagakure' the forty-seven rōnin. These were very idealized, and in some cases went against official shogunate policy such as with the 47 rōnin incident.

Wikipedia did include this unsourced claim as well:

Some samurai and even commoners also attended private academies, which often specialized in particular Japanese subjects or in Western medicine, modern military science, gunnery, or Rangaku (Dutch studies), as European studies were called.

Regrettably, the statement isn't dated to a specific period. It is my understanding that gunnery was extremely uncommon after the early-17th demilitarization. Similarly, "modern military science" isn't qualified in any way; it was my understanding that for most students of "Western studies", this was limited to the Dutch language, philosophy, and medicine, but I'm not sure. These subjects sound a lot more plausible after 1853 and modernization spurring from that.

Notable Military Events

Notable military events during the time period you quote of 1603–1868 include the Siege of Osaka and the Shimabara Rebellion in the early period. Four other rebellions are listed on Wikipedia for the time period, but one of them is linked to ronin, two to the Ainu, and only one could be considered a more popular uprising, channelling the feelings of Osaka.

An example of an independent han action (i.e., without shogunal troops but with the shogun's permission) is the 1609 invasion of Ryūkyū where Satsuma deployed its troops, in numbers they felt sufficient, to subjugate Ryūkyū (and successfully accomplished it).

After Perry's expedition in 1853, militarization proceeded quite fast, especially amongst the outside domains like Satsuma, Tosa, and Chōshū. However, the pro-Shogunate domains also modernized relatively fast—the primary success measure was not which side these domains supported but rather how actionary (vs reactionary) a government the han had. So, the outside domains had more to gamble. That said, many people even in those governments were anti-Western in their outlook, even if they liked their guns and artillery.

There's also the famous Shimonoseki incident where Chōshū tried to block off the Shimonoseki straits to foreign shipping. Allied foreign troops landed and conquered the artillery positions. As the original shelling of foreign ships was an unsanctioned move by Chōshū, the Shogun authorized a punitive expedition against the domain.

Creating the Imperial Army

The end of independent han armies in Japan came when the three main pro-Imperial domains of Satsuma, Tosa, and Chōshū 'donated' their armed troops to the Emperor. This created a nascent 'Imperial Army' which remained a very sectarian organization for several decades. This was primarily evident by the 'victorious' domains exerting undue influence in the Army and Navy, e.g. Yamagata Aritomo for hailing from Chōshū. Similarly, most naval commanders in the early years hailed from Tosa. It should be noted that when the Bakumatsu started, this was not necessarily the goal of the samurai leaders of the opposition to the Shogunate but rather a bottom-up endeavour that the domains were finally abolished (Sakamoto Ryōma being a good example).

1. The understanding of the people serving in each han would have been that their loyalty was to their lord and domain.

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Question #1:
What did the Japanese military do to maintain their fighting edge during the Edo era/Bakufu (1603-1868)?

The Edo period was marked by isolation. A period of cultural and economic achievement. War and Military were deemphasized. Swords long worn by Samurai were outlawed. Japan's military during this time did not "maintain their edge", they stagnated and lost parody with the outside world. When Commodore Perry's squadron of 4 steam ships sailed into Tokyo Bay, they did so actively threatening force, after having already occupied Japanese Territory (Ryukyus in the Bonin Islands) and demonstrating their modern offensive abilities. Japan accepted Perry's overtures ultimately because they believed they had no military option to do otherwise. So the Edo period de-emphisized Japan's military and ultimately 250 years of stagnation where Japan lost their military edge.

Question #2:
launching WW2 on a strategy of quick gains, then perimeter defense, thus ceding the initiative to the US afterwards. It's been long said that no one wins a war by just defense.

The same strategy worked successfully in the Japanese Russian war of 1904. It was a gamble to repeat the strategy against the United States but what was the alternative? Ending their war in China on unfavorable terms or, attack the US and greatly expand their empire to allow them self sufficiency. They chose the latter.

I would reject your premise that Japan ceded the initiative to the US after Pearl. Japan lost 6 of their 10 aircraft carriers at the Battles of Coral Sea and Midway. This was the heart of their Navy. Given Japan was a feudalistic agrarian economy confronting the largest manufacturing economic power of it's day; clearly Japan lost the initiative rather than ceding it. Japan's economy did not deliver a single capital ship to the war effort who's keel was laid after pearl harbor. The United States industry not only recovered most of the ships sunk at Pearl, but also delivered 10 battleships, more than 20 fleet carriers, 70 escort carriers, 30 cruisers and nearly 200 destroyers after pearl. Regardless of the professionalism of Japan's military, that advantage was not sufficient to overcome the industrial mismatch. (see US Navy during WWII )

Question #3:
over-complicated plans and strategies (Midway and Coral Sea had multiple battle groups with limited communication capabilities. No plan survives contact with the enemy would be basic Western military axiom there.

The facts are the United States had broken Japan's naval codes and knew about both Coral Sea and Midway operations. That's nearly an insurmountable advantage and thus the subsequent consequences don't reflect on Japan's military strategists or operational order of battle. It was their intelligence and counterintelligence organizations which failed Japan in both cases.

Question #4:
reliance on mass wave attacks, despite having seen the effect of machine guns in WW1.

I think this is a fair point. I always thought this a cultural bias. Pereffering agility and quickness over speed and firepower. It's reflected in several ways in choices Japan made in WWII. Including as you say their troops choosing to abandon their heavy weapons when marching into battle. I've also seen these decisions attributed to the Japanese troops lack of respect for their advisories. Japan on several occasions relied upon lighter maneuverable troops and machines and saw great returns for these choices early in the war. However you are right this hurt japan after the war got going.

Guadal Canal's waves of Japanese who left their heavy weapons behind rather carrying them through the jungle, paid a huge price. This was less of a theme when japan fought on the defensive. Then it was more about scarce resources which limited Japan's use of heavy weapons later in the war.

Question #5:
treatment of POWs.

I would argue Japan's mistreatment of POW's (systemic starvation, lack of medical resources, lack of transportation which necessitated death marches) says more about scant resources than it does about anything else. Japan barely could feed it's own population once the US war time embargos took place. They just didn't have the resources available to humanely treat POW's.

Comments:

from: Italian Philosophers 4 Monica note that the US has, on several times, gotten caught with its pants down, first in 1917 then 1942, then again 1950.

I wouldn't say the United States "got caught with its pants down" in WWI, WWII or Korea. Rather I would say the US was living devoid of pants in all three occasions. From The American Revolution (George Washington's farewell address) to WWII the United States was an isolationist country with no international defense treaties, philosophically opposed to involving itself in foreign wars. (WWI was an exception.) For this reason it did not maintain much of an army. On the eve of WWII for instance the United States army was about the size of Portugal's or Belgians. Not a player with the first tier militaries of the late 1930's. With Regards to Korea, I would note that after WWII the US scaled down it's army to pre WWII levels 900,000 men by June of 1950. The US strategiests thought post WWII would look alot like pre WWII where the US could concentrate on it's economy and trade and other than that ignore global security concerns. After North Korea's invasion of South Korea, Truman was shocked when the US navy informed him it had no capability to embargo North Korea as a response. The massive WWII navy no longer existed 5 years after the end of WWII. Korea is what really convinced the US it needed to maintain a military capability to fight a two front global war for generations. So to your point the Failures of WWI, WWII, Korean Wars weren't military failures to prepare; they reflected a philosophical failure to recognize America's need to to participate in global security given it's interests in global economy and markets.

from: Italian Philosophers 4 Monica
the thing is, for all their bravado and political stranglehold, Japan's armed forces weren't that experienced, China aside (1905 Russian War was a shorty).

On the eve of WWII japan had a very experienced and accomplished military.

1895 First Sino Japanese War. Japanese Victory 1902 - 1905 The Japanese Russo War.. Japan defeats it's first European power. 1910 Japan concludes the annexation of Korea, Japanese Victory
1914-1918 Japan participates in WWI attacking central power possessions in the Pacific, Including the first successful aircraft carrier based air-raids. 1918-1922 Japan's Military invades Siberia. 1930 Japan's Military puts down a rebellion in Taiwan 1931 Japan invades Manchuria setting up a puppet state 1937 Japan invades China, The Second Sino-Japanese War. 1940 Japan invades French Indochina (modern day vietnam).

When Japan attacked Pearl Harbor they had been at near continuous war for 45 years. Japan's military was not only capable and professional but also innovative.

Japan's equipment was modern and their grasp of modern warfare was on pare with the great powers of the day.. ( UK, Frane, Germany). Their officers were products of elite European and American Universities. Yamamoto for example attended Harvard University(1919-1921) as well as the US War College(1924). Japan placed great resources in it's military and saw a rapid acceleration of their capabilities as a result. While Japan was planning and executing the attack on pearl harbor by air, a feat few people in the west thought was possible, with a torpedo custom designed to level off in the shallow harbor. The United States for example went into WWII without a functioning torpedo. The US Navy dept was too cheap in the interwar period to thoroughly test it.

from: Italian Philosophers 4 Monica
Militaries have long memories and US is still driven by German WW2 tank doctrine for conventional.

True. Although Germany never dreamed of the kind of air support the US Air Force can provide with smart bombs, Nor the accuracy of modern artillery and rockets, Nor the speed and efficiency of modern tanks. But Yes you are correct basically the US still follows German WWII military doctrine of Blitzkrieg. I would also say that doctrine might be outdated now. Israel which also follows basically the same doctrine although at a much smaller scale, arguable lost their first war in 2008. Dec 2008, First time Israeli forces retired and left an enemy in the field. Israel lost more tanks in that three week war than the US lost in both gulf wars. These losses reflect the changing face of war rather than some shortcoming in the Israeli forces. Short range anti tank and anti personnel missiles fired from fortified positions might have flipped the advantage to the defenders even against air, ground superiority supported by artillery.

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