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This is literally my first foray into rom hacking and even with how easy HexManiacAdvanced has been I still have no idea what I'm doing.

I'm not making an entirely new game, just tweaking Vanilla GBA Sapphire into a more fun experience. Figured out how to change the starters (Chansey/Pikachu/Alolan Meowth), replaced "Boy" with Frisk from Undertale and am in the process of mangling the evolution charts into something that lets me have, say, an Absol that evolves into any one of the Legendary Beast Trio and an Arceusdamn male Salandit that actually evolves into an Arceusdamn Salazzle for the love of Arceus! YOU'RE NEXT GEN 3 FEEBAS! Oh do I have words for you ya' damn high beauty stat needing primadonna……

Anyway, Just need some help with minor tweaks and some fact checks. I'm sick to DEATH of Google and all these tutorials I'm finding not have the exact information I need. So I would be deeply grateful for any advice you guys can offer.

1.) TURNING OFF HMs….KIND OF….
What I would like to do is just add the overworld effects of HMs to regular moves, nothing too extreme, just have "Flash" be applied to moves like Ember and Thundershock. But if that's not an option I'd settle for disabling the flag code that prevents you from deleting HM moves manually.

2.) POSSIBLE NATIONAL POKEDEX ISSUES
As you probably guest by the Salazzle mention I'm gutting the Hoenn national dex of mons I don't want in favor of mons I do. But I'm worried this might cause problems with flag checking (or whatever it's called) regarding the local Hoenn Region Pokedex and evolving into mons not actually on it. I heard FireRed/LeafGreen has such a flag code so I just wanna make sure. Test playthroughs of the first few minutes had no problems but it'll be hours of gameplay before I can properly test the rest. Does Sapphire have flag code that prevents Pokemon not on the Hoenn dex from evolving in early game? Will it outright crash if I bring up the Pokedex?

Heck how do I even change the Pokedex entries? Probably have to swim through the damn ocean of code looking for the specific lines of text and edit them manually like I had to with the player sprites, what are the specific addresses?

3.) ALL THE EVOLUTION STONES I COULD EVER WANT
I still need to test out the new "Evolution Stones" I added to see if they work at all. I just copy pasted the HTML code of one and applied it to a bunch of ??'s I then renamed to stuff like "Rex Skull", "Dragonstone" and "Gamma Charge", will doing that copy pasting work fine or is that just a recipe in disaster? Or do I even need to do that? I noticed when I changed the evolution tab to "Stone" it brings up a mini tab listing all the items in the game. Is it even possible to just assign, say, a Heart Scale as a method of evolution? Or does it have be "EvolutionStone" specifically?

4.) CUSTOM MERCHANTS
Just how difficult is it to add in new venues to selling specific items? And is there a limit to how many items they sell?

5.) CHANGING KYOGRE & THE FOSSIL POKEMON
Tried to replace Lileep with Shieldon but the instant I tried editing the HTML code it didn't recognize "Shiedon" at all. Seemed to recognize Kabuto just fine. Did I just mess it up? Also is it even possible to replace the boss fight with Kyogre with any new Pokemon I put in?

6.) EXCLUSIVE BOSS BATTLES
Noticed a huge chunk of the actual Pokemon roster that is just a bunch of blanks, a whole section of "????s" sitting there doing nothing. Can't I just fill those with new mons or do they have to be blank for code stability? Actually even better, can't I just use those to input exclusive bosses and enemies that you can't actually catch?

Cause that's something I've always wanted to see in Pokemon, enemies and bosses you can't catch, only fight. They've only done it in small optional instances and I wish they did it more. One of my biggest pet peeves with Pokemon is how even the boss battles (i.e. Legendaries) are playable characters, kind of ruins the mystique of having bosses at all.
What I was thinking is having certain trainer battles have one non playable enemy or boss in their team with its own attacks and typing, like a soldier with an anti-Pokemon weapon or even a Team Rocket grade attack vehicle. In fact I was thinking of having Goku or Sailor Moon as trainers and then after you beat their actual Pokemon they just decide to jump in and fight your Pokemon on their own level! That would be awesome!

So yeah can't I just fill those "????s" in? Not even fully, just basic states, a single sprite and typing then just drop them into any trainer battle I want? Or does the game code require those spaces to be blank for stability purposes?

7.) CUSTOM STORY DIALOG
Exactly how much of the actual spoken dialog can I change before the game code defecates on the bed and stops working? Probably a stupid question but this is my first time with this sort of thing and I wanna make sure I don't mess up anything by accident.

And that's about it on the docket. Thank you for your time….