Nice ideas coachB - and good observations!
Maybe they'd be best off like the Franks? One battleboard, but different army compositions depending on the period being looked at. Perhaps there could be a Crusaders like mechanic of honour that the warlord gains during the battle and adds to certain abilities?
E.g. Early period - ashigaru are levy, samurai are warriors or hearthguard (elite e.g. hatamoto). All warrior and hearth guard samurai may be mounted. Only warrior class samurai on foot can have bows, but this does not reduce their armor by 1. Only mounted hearth guard samurai can have bows. This doesn't reduce their armor either. All mounted samurai are -1 armor to shooting. Make sure the battleboard has some abilities for "ashigaru", some for samurai, some for mounted, some for archery.
Late period - Levy are bow armed peasants. Ashigaru are spear armed warriors. Samurai are exclusively hearth guard and may be mounted. Samurai can take heavy weapons (naginata/tetsubo/nodachi) counting as dane axes. Samurai can take bows on horseback or teppo on foot. All mounted samurai are -1 armor to shooting. Ashigaru can take teppo too, but only one teppo armed unit (max size 8) is allowed per army. Teppo count as crossbows, but they don't reduce the armor of unit with them by 1. A late war samurai army *must* have at least one unit of hearth guard.