In M2TW you can't change the name of factions, so it would be difficult to have the Nagao clan becoming the Uesugi clan. It would also be a bit of a waste of a faction slot (remember: 31 factions is the max. number of factions, including the rebels) as the Nagao are close retainers of the Uesugi. Same with the Matsudaira/Tokugawa. You can only name the faction one of the two. You can pull of a trick where the surname of family members change from Matsudaira to Tokugawa though.
Nice. Yes, it's not that hard. I just started to doubt whether it was even possible at all or not as I haven't seen the sashimonos fixed in any Shogun 2 mod ever. Good to see that's fixed. Now I can lay down my OCD to rest.