These are all really fascinating questions! The lives of peasants is often overshadowed when looking into the history of Japan, which is often focused on through the frame of ‘samurai history’. Despite this, it is a topic which is very complex, and is very connected with other aspects of Japanese history. Before starting, I think it is important to note the huge scope that is called upon by some of the questions you have brought up. The 12th-17th century is a vast amount of time, spanning (and not exclusively) 3 different shogunates (Kamakura 1180s-1330s, Muromachi 1330s-1570s, and Edo bakufu 1600s-1860s). The condition of peasants varie heavily throughout this time, as well as throughout different regions of Japan in any given time. As a result the answers to the different questions you ask are dependent on several changing factors. As a result, I will try to give a overview of the history and of peasants in the different periods, and along the way will touch on different questions you have proposed.Before diving into the topic directly, it will be helpful to go through some different conditions and phenomenons that had major impact on the lives of peasants throughout the different periods. I will focus on two underlying societal shifts that occurred in the periods:
1.) The economical / administrative systems which were present, the shift being from the shōen system of Kamakura, which deteriorates during the Muromachi, and is replaced (in some regions) with the kandaka system implemented by many Sengoku daimyō, and finally the kokudaka system started by Hideyoshi, and used during the Edo period.
2.)The way in which society was organized, the shift being from centering around the shōen estates, to that of the villages (and sōsons (village communes)).
These different systems and conditions were currents which in many ways drove the lives of peasants throughout the periods. As stated by Nagahara Keiji in The Cambridge History of Japan Vol. 3, “The life of the peasants was defined by the continuities and changes in the authority systems of the medieval period.” ([1] pg. 303) It is because of this, that it is important to keep in mind these various shifting conditions, and they will be touched upon throughout the response.