Spotted a couple of things missing:
No yellow line between Koa and Patch, Koakuma is Patchouli's familiar, I think it's Grimore of Marisa that confirms it, if EoSD Stage 4 didn't make it obvious. Might be somewhere else that confirms it, but it's fairly soild.
Kogasa should be bunched with the Myouren crew really. Even if she was not related with them in UFO, by TD she's living in the graveyard of the temple. There is also no Kogasa-Yoshika line, despite the two fighting in TD. Failing that, seeing as Reimu/Sanae/Marisa beat her up on sight, even when she asks them for help, they have an antagonistic relationship.
Also Kogasa/Human Village seem to be on alright terms, since human children like her, as stated in the recent thingy I forgot the name of.
Things which are more subjectives and based on points of view:
Probably safe to assume Suwako knows Hina, in fact, since Hina is a Curse Goddess and Suwako can control them...
Seiga/Kasen seem on good terms, if Kasen is wondering what's so wicked about her.
Kanako-Sanae seems master-servant
Nue's not really under Byakuren's control, at least, from what I understand. Mamizou certainly isn't, she's only linked to Myouren because of Nue.