Sorry I never saw your post. I have been playing TRE for about a week and I think I have figured most of the game out. Basically ignore the entire plot line and keep raising your Pokémon by moving on. Eventually, you will get to the Celadon equivalent city (name I have forgotten) and just like in RBY you have to attack the secret building in the Game Corner. Only in this game, it is owned by the police and not by Team Rocket. Play though it (Same map as in RBY but Pokémon are in the low to mid 40s) to receive the GHOSE SCOPE. Then head back to the Pokémon Cemetery (where the Pokémon tower is) and proceed through to get the Poke Flute. (Note your rival has Pokémon in here level 20s so they are good to train new Pokémon on) The trainers in here all have gastlys or Haunters all between level 33-38 and wild Pokémon are same level. Once you clear the Mother Marowak, the trainers hold mid 40s Pokémon of various types (Nidos, Ninetales, two Haunters, Rhyhorn etc).
If you have any other questions, plz feel free to PM me or send anyone else you know with questions to me