Well, it's quite a lot indeed to start over. I'm assuming you didn't backup ever, right?
Look, first thing you should try - after making a backup - is going to the Pokémon between Celebi and Treecko and make them be ??? again.
Make a backup first and then try doing this. Let's see if that's enough.
I replaced some of the pokemon from the hoenn region, I edited the hex of the rom to make mew obey, and let pokemon evolve without national dex.
I also used a-map to create some events and change wild pokemon data. And used some of the ??? between celebi and treeko to add some pokemon. I also edited alot of the trainers using G3T using your ini. Thanks alot man!