I like the two ideas you have, i think the skaven should show up at some period in clan eshin finding Nippon and causing some minor cultural exchange with the peasantry? I'm not sure if you planned to expand on the fluff for specific shoguns or clans.
Having a period time with a few major clans warring or perhaps alliances of clans warring (think romance of the three kingdoms, but obviously japan and not china) could be interesting and used to expand on some differences between clans, fighting styles/specialties. Other than that maybe write up some specific event story's that focus on a legendary warrior. Both of these ideas could be written in a pseudo historical fashion that is highly shrouded in unknowns and with a solid amount of dramatization/exaggeration. for a legendary warrior it could be, unscrupulous daimyo X was a bad dude but didn't directly go against bushido, none in his domain could stand up to him so when he sent a force to subdue some villages that stopped paying the exorbitant tithes he demanded, one of his samurai (a legendary warrior perhaps) defied him and defended the village against all the lesser samurai the daimyo sent until he came himself and was also defeated. Think 'lone samurai' legends.
sorry I can't be more help, thats a pretty massive time period to fill, good luck