You should try loader gx to see if it black screens as well, If it doesn't it would mean it's an issue with wiiflow.
First, you should update nintendont, then..did you enable autoboot in cfg? It sounds like even if you choose the game in the loader, you have to pick it again, i might have misread that though.
You should delete nincfg.bin if there's one in your hdd. That could cause errors, especially if cfg wasn't updated to work with the new configs in Nintendont (i don't use it so i don't know how updated it is).
Finally, as Howard said, your priority should be to get Nintendont itself to find your hdd, remember it should be a primary partition formatted as fat32. If there isn't a mounted drive where the mc can be stored, it's logical that nintendont would crash.
Edit: also, if it were me, i wouldn't have spent 6 hs putting everything back, instead i'd copy one or two games and make sure the hdd is working before. An alternative is to just use another loader