I looked through the save - you have, in fact, completed everything up to the endgame. The fact that the items are saying "advance other quests" might be slightly misleading - they're waiting for you to "advance" the Ned Endgame quest so that that quest can close them.
In retrospect, it would probably have been better to have those quests "self-close," but the combination of the way the writer was advancing things and the way I coded this game didn't make that easy. Apologies. (Season 2 is coded quite differently, which helps avoid this kind of thing.)