Burned tower
Well... this is the best hack ever but I suppose that u already know that...
Just wanted to say that I think u made a mistake in the burned tower (it is not a glitch):
After u beat Silver in Burned Tower, for meeting the Legendary dogs/cats/things u must use rock smash, but for using rock smash outside battle u must have another badge (I think it's olivine's gym's medal). And this is a place to visit even before beating morty, since the level of Silver's pokemons is lower than those of morty.
Summarizing, the problem is a little rock that u should take away, also, this rock wasn't there in G/S/C (anyway it wouldn't have been a problem since in those games rock smash wasn't a HM).
Appart from that, congratulations for making the best hack ever!