You don't have to start over! Just copy the game.rxdata over to the new folder.
However I've hit a roadblock...literally.
The area near a ladder in the jungle cave and another area in the jungle cave where the bug blockade is, each time I get even a little close the entire game crashes and I have to refresh my system just to be able to move the mouse/cursor.
I'm not sure what I should do...
Hmm... I think it might just be that your computer can't handle having that many animated sprites on screen at once. Try playing on a different computer, if possible; you can copy the save file over.
In any case, you got very far, almost to the end, so kudos! What team of Pokemon did you use?