I'm just planning to use A-Text right now, I should be able to find the entries of the pokemon that was replaced using the search function, and cross-reference the normal hoenn dex with Wes's additions to add the right ones. Using YAPE on this hack means death because of the 27 extra slots, and I don't know any other tool that does it.
The only thing is, I have no idea how to edit the Pokedex entries for those extra slots, or even if they have pokedex entries to begin with. One might show up when you catch them, I'm not sure. I don't even know how to test that, because I don't know how I'd go about using a gameshark code when the slots weren't in use in the source game... I guess I could test Reshiram, but ugh, new save file, effort. I think I'll just ignore them, or maybe go exploring on YAPE with a copied file. :)