Candid,
Actually cutting into farming really isn't all that accurate. The Thirty Years War was an extreme example of continuous warfare. It takes a lot of killing to depopulate a third of the male population of a country, and even that doesn't have a huge impact on farming. In the entire Civil war only 3% of America's population at the time were killed, and that was one bloody war.
So each province should have a number of draft age men, say, with 120 man units.... 40,000 men of draft age (this is in one of the bigger provinces, like Dewa or Iyo). Keep in mind that this number should be increasing continually, with, maybe, 1-200 men coming of age each year. These are very wild and inaccurate estimates, since I have absolutely no data on Japan's population at the time, the birth rate, or the draft age.
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