Japan in the earliest start date would be in the Nara period, which historically lasted until 794. At that time, Japan was still looking for a definite way to shape itself. It had a system which was one the hand very much like that of China but on the other hand traces of Japanese aristocracy were still present. At this time, heavy contact with China was maintained. As early as 723 a law was passed that said that anyone who invested in creating new farmland would own said farmland for three generations. In 743, when the former law didn't get enough people to invest, it was changed so that anyone who invested would hold the land indefinitely. And guess who had the most money. Yes, that's right, the aristocrats and the temples. This reform was in stark contrast to the Taika reforms which modeled the Japanese government more on the system the Chinese used.
Army-wise, the Japanese had a system which, similarly to the Chinese, required each family to provide on soldier for so many years or pay a tax. By 774 the Emishi would still conduct regular raids, particularly in the Kantou region, but the rest of the tribes had been pacified. Since the imperial court was located in Nara (same as present day Nara) they abolished their military system and only kept it in the border provinces which stood to benefit from a permanent garrison. By 804, the Emishi had been subjugated.
Politically, there were three factions vying for control. The emperor (and the imperial family), the aristocracy and the temples. Eventually the aristocracy (Fujiwara) won this game of court intrigue and came to dominate politics in Japan.
Historically the next period in Japanese history is the Heian period, which is after the capital was moved to Heian (present day Kyouto). Formal contacts with the Chinese were severed, although there was still interaction between the two countries through trade, piracy and scholars. The Heian period is usually seen as the period of Japanese court culture, with many famous works of writing, think Genji Monogatari, coming from this period. These works were, notably, written in Japanese rather than in Chinese. The bureaucratic ranks and institutions that were introduced with the Taika reforms continued to exist, but getting a high rank didn't mean an increase in power and income, it rather confirmed that power that an aristocrat already had at his birth. As said before, this period was largely dominated by the Fujiwara. The head of the family would marry their daughters to emperors so that the Fujiwara head would be the grandfather of the next emperor, and due to the Confucian ideology the emperor thus had to listen to the head of the Fujiwara. Also, the Fujiwara would be the regent of an underage emperor most of the time, and later on they even managed to remain regents for the rest of their lives (talk about long lasting regencies). There was resistance to this, and some emperor did manage to temporarily rule on their own, but this never lasted. At the same time, the growth of the private farmland went on and this in turn caused powerful landlords to appear.
Army-wise, the armies of the Nara period had been abolished and lower nobles who had undergone training with weapons in their own time acted as police in this time period. These are early samurai, but the fact that they were of low rank and lacked any real organisation meant that they had no power. It should be noted, by the way, that Japanese nobles at this time were not expected to be able to fight, as was the case in Europe. At the end of the ninth century, these warriors started forming small coalitions. By 935, these coalitions had grown considerably in size and some were able to field a thousand riders. Leaders of these coalitions also rebelled, and one, Taira no Masakado (not of the famous Taira family), even proclaimed himself emperor. The armies of the actual emperor consisted mostly of the same type of warriors, with the only difference being that these armies were led by high ranking nobles who held actual titles. By the eleventh century, two warrior families had risen to the forefront. These were both descendants of the Imperial line and were called, as you probably guessed, the Taira and the Minamoto. Both of these families supported an emperor during the Genpei war (1156-1192), a civil war between the Taira and the Minamoto. It should be noted that samurai in these times were nobles first, and warriors second. Eventually the Minamoto won, the first shougnate was created and the de-facto capital moved to Kamakura. After this, Japan is feudal.
All of this information is taken from Keizers en Shogun (Emperors and Shogun) by W.J. Boot.
So as for mechanics... Seeing how Japan is heavily reliant on Chinese systems in the earlier periods, it might be a good idea to add China first and then make Japan a sort of hybrid, with decisions or events slowly forcing Japan to the feudal side.
The problem Japan faces from a gameplay perspective is that it's not so much that the ruling family changes, but that the entire system changes. While it would be fun to play emperor in the Nara period, by the time the Kamakura period comes around the position would have been marginalized so much you wouldn't be able to do anything. The same goes for the Fujiwara which are only really influential in the Heian period, and the samurai don't become truly influential until the eleventh century.
As for the Mongol invasions, remember that it were the storms who destroyed those Mongol boats, twice. The Japanese, however, were woefully unprepared for an organized Mongol invasion and would probably have been utterly crushed if it weren't for those storms.
