A kinda out of nowhere question, but what do you imagine the actual daily jobs/duties are for the Links in your post manga scenario?
Immediately after their adventure (assuming an AU where they stay separate), everyone is pretty thoroughly occupied with rebuilding. They spend a lot of time clearing rubble, sorting out what can be salvaged from destroyed buildings, etc.
In the slightly-longer term, they continue training as knights. They're in this sort of awkward middle space where they are still too young to be considered full knights (and their dad has always been pretty adamant about not letting Link skip ahead), but they've also spent so much time around the knights since Link was an infant, and they are also now heroes of Hyrule. So they're not quite full knights, but they're still higher ranking and more experienced than the other trainees (and, frankly, most full knights).
So they do still have some classes with the trainees, but at other times they're the ones doing the mentoring. It's also not unusual for the them to go on missions together, if there's been monster trouble somewhere in Hyrule.
Over time they each start focusing more on their own strengths and interests, too:
Green helps his father with the logistical side of being captain of the knights, and is being tutored on diplomacy (something Link never paid much attention to before xD )
Blue spends a lot of time in the training fields, both honing his own skills and teaching others
Red focuses on practicing with his magic, at first out of anxiety of losing control of it, but he soon discovers a passion for the ways fire can be used constructively, such as metalworking, glassblowing, etc.
Vio, of course, spends a lot of time in the library, both doing his own research and helping the librarian there. Occasionally Zelda will ask him for help gathering information she needs for some decision. Usually through legitimate channels. Usually.
As for Shadow, well... most of the rest of Hyrule considers themself content as long as his daily activities don't result in any explosions, or at least not of anything important ^^;; Sometimes he trains with the other Links. Sometimes he helps Red with his magic practice. Sometimes he follows Vio around. Sometimes he disappears for stretches of time (these stretches of time frequently line up with Vio having new information for Zelda from unknown sources)
