Well it's a no to the time travel idea, as the 'time travel' is brought to the Hyrule in the game when Ganondorf enters the sacred realm and characters from many Zelda games and timelines are brought into the one world. As far as Link obtaining the gems, there was a plan for them to exist around as a natural resource used as something else for people without the power of the Triforce, but I think it should be scrapped. I was thinking along the same lines as you with the Zoras being able to capture the monsters, more specifically the Gerudo, since it'd still be awesome to have a Gerudo join your team. The human monsters for the most part wouldn't evolve though.
I do edit my textboxes in NSE lol. I actually use NSE to do all of my palette editing instead of APE because it's much more stable. I'll try messing with the palettes of some of the other boxes if that's what you mean though, thanks :D
EDIT: Just finished the second evo for this chain, dubbed just "Goron".
aaand the backsprites shinies and minisprites: