So thankfully this scenario has never happened to me yet because I honestly don't know what would result. Say I have Herald of Perfection on my field and set backup soldier. I also have no fairies in my hand to negate an effect that would destroy Herald, however, I do have 5 fairies in my graveyard: 3 mystical shine balls, 1 honest, and 1 manju of the ten thousand hands. Say my opponent decides they don't like Herald and activate dark hole. Would I be able to chain backup soldier, get 3 shine balls to my hand, and then activate Herald's effect after backup soldier resolves to negate the activation of dark hole? Basically what i'm asking is, can I chain within a chain if it's not fully resolved yet? (I hope i'm wording this right)

Nope, you wouldn't be able to. Once a chain starts resolving, you can't chain cards until it's finished resolving. As such, Soldier would resolve and add stuff, then Dark Hole would resolve and kill Herald

Just another question that came to mind. If say I activate fiendish chain on Herald, then Herald attempts to negate it, can I chain Mist Valley Thunder Lord to Herald's effect to return fiendish chain back to my hand? (assuming Herald wouldn't just negate Mist Valley Thunder Lord's effect if its legal)

You guys are life savers :3